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Center for Nonlinear Studies |
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimizing algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition algorithm which is a combinationof a heterogeneity sensitive spatial domain decomposition with an a priori sliding subdomain-walls procedure. The algorithm modeling is presented for dual resolution systems and inhomogeneous binary fluids, in terms of scaling properties as a function of the size of the low-resolution region and the high to low resolutions ratio. We also show the algorithm competences, by comparing it to its initial domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.
Host: Christoph Junghans