TY - CONF AB - We present the submatrix method, a highly parallelizable method for the approximate calculation of inverse p-th roots of large sparse symmetric matrices which are required in different scientific applications. Following the idea of Approximate Computing, we allow imprecision in the final result in order to utilize the sparsity of the input matrix and to allow massively parallel execution. For an n x n matrix, the proposed algorithm allows to distribute the calculations over n nodes with only little communication overhead. The result matrix exhibits the same sparsity pattern as the input matrix, allowing for efficient reuse of allocated data structures. We evaluate the algorithm with respect to the error that it introduces into calculated results, as well as its performance and scalability. We demonstrate that the error is relatively limited for well-conditioned matrices and that results are still valuable for error-resilient applications like preconditioning even for ill-conditioned matrices. We discuss the execution time and scaling of the algorithm on a theoretical level and present a distributed implementation of the algorithm using MPI and OpenMP. We demonstrate the scalability of this implementation by running it on a high-performance compute cluster comprised of 1024 CPU cores, showing a speedup of 665x compared to single-threaded execution. AU - Lass, Michael AU - Mohr, Stephan AU - Wiebeler, Hendrik AU - Kühne, Thomas AU - Plessl, Christian ID - 1590 KW - approximate computing KW - linear algebra KW - matrix inversion KW - matrix p-th roots KW - numeric algorithm KW - parallel computing SN - 978-1-4503-5891-0/18/07 T2 - Proc. Platform for Advanced Scientific Computing (PASC) Conference TI - A Massively Parallel Algorithm for the Approximate Calculation of Inverse p-th Roots of Large Sparse Matrices ER - TY - JOUR AB - A numerically efficient yet highly accurate implementation of the crystal orbital Hamilton population (COHP) scheme for plane-wave calculations is presented. It is based on the projector-augmented wave (PAW) formalism in combination with norm-conserving pseudopotentials and allows to extract chemical interactions between atoms from band-structure calculations even for large and complex systems. The potential of the present COHP implementation is demonstrated by an in-depth analysis of the intensively investigated metal-insulator transition in atomic-scale indium wires self-assembled on the Si(111) surface. Thereby bond formation between In atoms of adjacent zigzag chains is found to be instrumental for the phase change. © 2017 Wiley Periodicals, Inc. AU - Lücke, Andreas AU - Gerstmann, Uwe AU - Kühne, Thomas D. AU - Schmidt, Wolf G. ID - 13238 IS - 26 JF - Journal of Computational Chemistry KW - density functional theory KW - bonding KW - crystal orbital Hamilton population KW - indium nanowires KW - phase transition TI - Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) – (4 × 1) phase transition VL - 38 ER - TY - JOUR AU - Azadi, Sam AU - Kühne, Thomas D. ID - 13239 IS - 8 JF - The Journal of Chemical Physics TI - High-pressure hydrogen sulfide by diffusion quantum Monte Carlo VL - 146 ER - TY - JOUR AU - Lücke, Andreas AU - Gerstmann, Uwe AU - Kühne, Thomas D. AU - Schmidt, Wolf Gero ID - 13417 JF - Journal of Computational Chemistry SN - 0192-8651 TI - Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) - (4 × 1) phase transition ER - TY - JOUR AU - Zimmer, Peter AU - Müller, Patrick AU - Burkhardt, Lukas AU - Schepper, Rahel AU - Neuba, Adam AU - Steube, Jakob AU - Dietrich, Fabian AU - Flörke, Ulrich AU - Mangold, Stefan AU - Gerhards, Markus AU - Bauer, Matthias ID - 16319 JF - European Journal of Inorganic Chemistry SN - 1434-1948 TI - N-Heterocyclic Carbene Complexes of Iron as Photosensitizers for Light-Induced Water Reduction ER - TY - JOUR AB - Recently, the quantum harmonic oscillator model has been combined with maximally localized Wannier functions to account for long-range dispersion interactions in density functional theory calculations (Silvestrelli, J. Chem. Phys. 2013, 139, 054106). Here, we present a new, improved set of values for the three parameters involved in this scheme. To test the new parameter set we have computed the potential energy curves for various systems, including an isolated Ar2 dimer, two N2 dimers interacting within different configurations, and a water molecule physisorbed on pristine graphene. While the original set of parameters generally overestimates the interaction energies and underestimates the equilibrium distances, the new parameterization substantially improves the agreement with experimental and theoretical reference values. © 2016 Wiley Periodicals, Inc. AU - Partovi-Azar, Pouya AU - Berg, Matthias AU - Sanna, Simone AU - Kühne, Thomas D. ID - 13240 IS - 15 JF - International Journal of Quantum Chemistry KW - Wannier orbitals KW - Van der Waals interactions KW - density functional theory KW - quantum harmonic oscillator TI - Improved parameterization of the quantum harmonic oscillator model based on localized wannier functions to describe Van der Waals interactions in density functional theory VL - 116 ER - TY - JOUR AB - The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. AU - Köster, Andreas AU - Spura, Thomas AU - Rutkai, Gábor AU - Kessler, Jan AU - Wiebeler, Hendrik AU - Vrabec, Jadran AU - Kühne, Thomas D. ID - 13241 IS - 19 JF - Journal of Computational Chemistry KW - liquid water KW - force matching KW - ab initio KW - molecular dynamics KW - Monte Carlo TI - Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations VL - 37 ER - TY - JOUR AU - John, Christopher AU - Spura, Thomas AU - Kühne, Thomas D. ID - 45766 JF - Phys. Rev. E TI - Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab Initio molecular dynamics VL - 93 ER - TY - CONF AU - Lass, Michael AU - Kühne, Thomas AU - Plessl, Christian ID - 25 T2 - Workshop on Approximate Computing (AC) TI - Using Approximate Computing in Scientific Codes ER - TY - JOUR AU - Elgabarty, Hossam AU - Khaliullin, Rustam Z. AU - Kühne, Thomas D. ID - 34310 IS - 1 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry SN - 2041-1723 TI - Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments VL - 6 ER - TY - JOUR AU - Calcavecchia, Francesco AU - Pederiva, Francesco AU - Kalos, Malvin H. AU - Kühne, Thomas D. ID - 45767 JF - Phys. Rev. E TI - Sign problem of the fermionic shadow wave function VL - 90 ER - TY - JOUR AU - Richters, Dorothee ID - 45768 JF - J. Chem. Phys. TI - Self-consistent field theory based molecular dynamics with linear system-size scaling VL - 140 ER - TY - JOUR AU - Kühne, Thomas D. AU - Khaliullin, Rustam Z. ID - 45769 JF - Nature Commun. TI - Electronic signature of the instantaneous asymmetry in the first coordination shell of liquid water VL - 4 ER -