Optimization of SHAKE and RATTLE Algorithms

SHAKE and RATTLE algorithms are widely used in molecular dynamics simulations and for this reason are relevant for a broad range of scientific applications. In this work, an existing CPU+GPU implementations of the SHAKE and RATTLE algorithms from the DL_POLY application are investigated. DL_POLY is a general purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith and I.T. Todorov. OpenCL code of the SHAKE algorithm for DL_POLY application is analyzed for further optimization possibilities. Our work with RATTLE algorithm is focused on porting of the algorithm from Fortran to OpenCL and adjusting it to the GPGPU architecture.