ABSTRACT
Department of Computer Science, University of Illinois at Urbana-Champaign
Abhinav Bhatele
Center for Applied Scientific Computing, Lawrence Livermore National Laboratory
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 5.2 Car-Parrinello Molecular Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
5.2.1 Density Functional Theory, KS Density Functional Theory and the Local Density Approximation . . . . . . . . . . 82
5.2.2 DFT Computations within Basis Sets . . . . . . . . . . . . . . . . . . . 84 5.2.3 Molecular Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 5.2.4 Ab initio Molecular Dynamics and CPAIMD . . . . . . . . . . . 84 5.2.5 Path Integrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 5.2.6 Parallel Tempering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5.3 Parallel Application Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 5.3.1 Modular Design and Benefits . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 5.3.2 Parallel Driver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.3.2.1 Decomposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 5.3.2.2 Control Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 5.3.2.3 Multiple Interacting Instances . . . . . . . . . . . . . 92
5.3.3 Topology Aware Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 5.4 Charm++ Feature Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 5.5 Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 5.6 Impact on Science and Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
5.6.1 Carbon Based Materials for Photovoltaic Applications . 98 5.6.2 Metal Insulator Transitions for Novel Devices . . . . . . . . . . 102
5.7 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Parallel Approach
OpenAtom is parallel simulation software for studying atomic and molecular systems based on quantum chemical principles. In contrast to classical computational molecular dynamics which is based on Newtonian mechanics, OpenAtom uses the Car-Parrinello ab initio Molecular Dynamics (CPAIMD) approach. This allows it to study complex atomic and electronic physics in semiconductor, metallic, biological and other molecular systems. The application has been designed to expose maximal parallelism via small grains of data and computation. The resulting implementation atop Charm++ is highly scalable, and has exhibited portable performance across three generations of the IBM Blue Gene family, apart from other supercomputing platforms.
