Parallel implementations of Molecular Dynamics (MD) simulation (Lennard-Jones potential) in C++, supporting optional features such as neighbors list, blocks (loop tiling), and cells (space decomposition).
The implementations provides the needed API to target shared memory systems, distributed memory systems, or both (the loop body of the simulation needs to be adapted depending on the target platform).
The source code is available through Git, using URL git://alba.di.uminho.pt/case-studies/jgf-cpp/moldyn-spl.git (more details here). It can also be downloaded directly from here.
(This software was originally based on the Java Grande Forum Benchmark Suite – moldyn case study.)
This work was funded by ERDF – European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-010152.