@inproceedings{NoackReinefeldKrameretal., author = {Noack, Matthias and Reinefeld, Alexander and Kramer, Tobias and Steinke, Thomas}, title = {DM-HEOM: A Portable and Scalable Solver-Framework for the Hierarchical Equations of Motion}, series = {2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018)}, booktitle = {2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 19th IEEE Int. Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC 2018)}, isbn = {978-1-5386-5555-9}, doi = {10.1109/IPDPSW.2018.00149}, pages = {947 -- 956}, abstract = {Computing the Hierarchical Equations of Motion (HEOM) is by itself a challenging problem, and so is writing portable production code that runs efficiently on a variety of architectures while scaling from PCs to supercomputers. We combined both challenges to push the boundaries of simulating quantum systems, and to evaluate and improve methodologies for scientific software engineering. Our contributions are threefold: We present the first distributed memory implementation of the HEOM method (DM-HEOM), we describe an interdisciplinary development workflow, and we provide guidelines and experiences for designing distributed, performance-portable HPC applications with MPI-3, OpenCL and other state-of-the-art programming models. We evaluated the resulting code on multi- and many-core CPUs as well as GPUs, and demonstrate scalability on a Cray XC40 supercomputer for the PS I molecular light harvesting complex.}, language = {en} } @article{KramerNoackReinefeldetal., author = {Kramer, Tobias and Noack, Matthias and Reinefeld, Alexander and Rodr{\´i}guez, Mirta and Zelinskyi, Yaroslav}, title = {Efficient calculation of open quantum system dynamics and time-resolved spectroscopy with Distributed Memory HEOM (DM-HEOM)}, series = {Journal of Computational Chemistry}, volume = {39}, journal = {Journal of Computational Chemistry}, number = {22}, publisher = {Wiley Periodicals, Inc.}, doi = {doi:10.1002/jcc.25354}, pages = {1779 -- 1794}, abstract = {Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes.}, language = {en} } @article{KramerNoackReimersetal., author = {Kramer, Tobias and Noack, Matthias and Reimers, Jeffrey R. and Reinefeld, Alexander and Rodr{\´i}guez, Mirta and Yin, Shiwei}, title = {Energy flow in the Photosystem I supercomplex: comparison of approximative theories with DM-HEOM}, series = {Chemical Physics}, volume = {515}, journal = {Chemical Physics}, publisher = {Elsevier B.V.}, doi = {10.1016/j.chemphys.2018.05.028}, pages = {262 -- 271}, abstract = {We analyze the exciton dynamics in PhotosystemI from Thermosynechococcus elongatus using the distributed memory implementation of the hierarchical equation of motion (DM-HEOM) for the 96 Chlorophylls in the monomeric unit. The exciton-system parameters are taken from a first principles calculation. A comparison of the exact results with Foerster rates and Markovian approximations allows one to validate the exciton transfer times within the complex and to identify deviations from approximative theories. We show the optical absorption, linear, and circular dichroism spectra obtained with DM-HEOM and compare them to experimental results.}, language = {en} }