@inproceedings{1590, abstract = {{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.}}, author = {{Lass, Michael and Mohr, Stephan and Wiebeler, Hendrik and Kühne, Thomas and Plessl, Christian}}, booktitle = {{Proc. Platform for Advanced Scientific Computing (PASC) Conference}}, isbn = {{978-1-4503-5891-0/18/07}}, keywords = {{approximate computing, linear algebra, matrix inversion, matrix p-th roots, numeric algorithm, parallel computing}}, location = {{Basel, Switzerland}}, publisher = {{ACM}}, title = {{{A Massively Parallel Algorithm for the Approximate Calculation of Inverse p-th Roots of Large Sparse Matrices}}}, doi = {{10.1145/3218176.3218231}}, year = {{2018}}, } @article{13238, abstract = {{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.}}, author = {{Lücke, Andreas and Gerstmann, Uwe and Kühne, Thomas D. and Schmidt, Wolf G.}}, journal = {{Journal of Computational Chemistry}}, keywords = {{density functional theory, bonding, crystal orbital Hamilton population, indium nanowires, phase transition}}, number = {{26}}, pages = {{2276--2282}}, title = {{{Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) – (4 × 1) phase transition}}}, doi = {{10.1002/jcc.24878}}, volume = {{38}}, year = {{2017}}, } @article{13239, author = {{Azadi, Sam and Kühne, Thomas D.}}, journal = {{The Journal of Chemical Physics}}, number = {{8}}, pages = {{084503}}, title = {{{High-pressure hydrogen sulfide by diffusion quantum Monte Carlo}}}, doi = {{10.1063/1.4976836}}, volume = {{146}}, year = {{2017}}, } @article{13417, author = {{Lücke, Andreas and Gerstmann, Uwe and Kühne, Thomas D. and Schmidt, Wolf Gero}}, issn = {{0192-8651}}, journal = {{Journal of Computational Chemistry}}, pages = {{2276--2282}}, title = {{{Efficient PAW-based bond strength analysis for understanding the In/Si(111)(8 × 2) - (4 × 1) phase transition}}}, doi = {{10.1002/jcc.24878}}, year = {{2017}}, } @article{16319, author = {{Zimmer, Peter and Müller, Patrick and Burkhardt, Lukas and Schepper, Rahel and Neuba, Adam and Steube, Jakob and Dietrich, Fabian and Flörke, Ulrich and Mangold, Stefan and Gerhards, Markus and Bauer, Matthias}}, issn = {{1434-1948}}, journal = {{European Journal of Inorganic Chemistry}}, pages = {{1504--1509}}, title = {{{N-Heterocyclic Carbene Complexes of Iron as Photosensitizers for Light-Induced Water Reduction}}}, doi = {{10.1002/ejic.201700064}}, year = {{2017}}, } @article{13240, abstract = {{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.}}, author = {{Partovi-Azar, Pouya and Berg, Matthias and Sanna, Simone and Kühne, Thomas D.}}, journal = {{International Journal of Quantum Chemistry}}, keywords = {{Wannier orbitals, Van der Waals interactions, density functional theory, quantum harmonic oscillator}}, number = {{15}}, pages = {{1160--1165}}, title = {{{Improved parameterization of the quantum harmonic oscillator model based on localized wannier functions to describe Van der Waals interactions in density functional theory}}}, doi = {{10.1002/qua.25150}}, volume = {{116}}, year = {{2016}}, } @article{13241, abstract = {{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.}}, author = {{Köster, Andreas and Spura, Thomas and Rutkai, Gábor and Kessler, Jan and Wiebeler, Hendrik and Vrabec, Jadran and Kühne, Thomas D.}}, journal = {{Journal of Computational Chemistry}}, keywords = {{liquid water, force matching, ab initio, molecular dynamics, Monte Carlo}}, number = {{19}}, pages = {{1828--1838}}, title = {{{Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations}}}, doi = {{10.1002/jcc.24398}}, volume = {{37}}, year = {{2016}}, } @article{45766, author = {{John, Christopher and Spura, Thomas and Kühne, Thomas D.}}, journal = {{Phys. Rev. E}}, title = {{{Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab Initio molecular dynamics}}}, volume = {{93}}, year = {{2016}}, } @inproceedings{25, author = {{Lass, Michael and Kühne, Thomas and Plessl, Christian}}, booktitle = {{Workshop on Approximate Computing (AC)}}, title = {{{Using Approximate Computing in Scientific Codes}}}, year = {{2016}}, } @article{34310, author = {{Elgabarty, Hossam and Khaliullin, Rustam Z. and Kühne, Thomas D.}}, issn = {{2041-1723}}, journal = {{Nature Communications}}, keywords = {{General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry}}, number = {{1}}, publisher = {{Springer Science and Business Media LLC}}, title = {{{Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments}}}, doi = {{10.1038/ncomms9318}}, volume = {{6}}, year = {{2015}}, }