Molecular Simulations as test beds for bridging High Throughput and High Performance computing

Abstract

The theoretical foundationsand the computing paradigms employed for the assemblage of the components of the Grid Empowered Molecular Simulator GEMS are described in Chapter 1. In that chapter the development of grid based workflows allowing the ab initio evaluation of the observable properties of small chemical systems starting from the calculation of the electronic properties is illustrated. In Chapter 2 the issue of the of interoperability between computational codes across different stages of the workflow is faced. The Chapter proposes Q5cost and D5cost common data modesl as de facto standard formats for quantum chemistry calculations. Chapter 3 relates to the results of standalone ab initio calculations performed on different small chemical systems (X4 clusters and BeH  dimer). The Chapter discusses particular and interesting chemical bonds requiring high-level quantum methods to the end of being rationalized. Finally Chapter 4 and Chapter 5 report the results of our work on two com- bustion and atmospheric chemistry problems (CH3CH2OO• isomerization and N2+N2 reaction) respectively. They both aim at constructing the PES for a reactive process. Once a PES is generated, the kinetic and dynamical data needed to be calculated for a large number of initial conditions can be computed on HTC platforms. The assemblage of the computational workflows for the coupled use of HPC and HTC systems is also dealt there.