Related papers: Million-atom molecular dynamics simulation by orde…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
A massively parallel order-N electronic structure theory was constructed by an interdisciplinary research between physics, applied mathematics and computer science. (1) A high parallel efficiency with ten-million-atom nanomaterials was…
The O(N) and parallelization techniques have been successfully applied in tight-binding molecular-dynamics simulations of single-walled carbon nanotubes (SWNTs) of various chiralities. The accuracy of the O(N) description is found to be…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
We present a method for total energy minimizations and molecular dynamics simulations based either on tight-binding or on Kohn-Sham hamiltonians. The method leads to an algorithm whose computational cost scales linearly with the system…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
The past years have witnessed impressive advances in electronic structure calculation, especially in the complexity and size of the systems studied, as well as in computation time. Linear scaling methods based on empirical tight-binding…
Several methodologies are developed for large-scale atomistic simulations with fully quantum mechanical description of electron systems. The important methodological concepts are (i) generalized Wannier state, (ii) Krylov subspace and (iii)…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
We describe how long-term solar system orbit integration could be implemented on a parallel computer. The interesting feature of our algorithm is that each processor is assigned not to a planet or a pair of planets but to a time-interval.…
We introduce a protocol for the fast simulation of $n$-dimensional quantum systems on $n$-qubit quantum computers with tunable couplings. A mapping is given between the control parameters of the quantum computer and the matrix elements of…
Using a real-space high order finite-difference approach, we investigate the electronic structure of large spherical silicon nanoclusters. Within Kohn-Sham density functional theory and using pseudopotentials, we report the self-consistent…
The integration of density functional theory (DFT) with machine learning enables efficient \textit{ab initio} electronic structure calculations for ultra-large systems. In this work, we develop a transfer learning framework tailored for…
Ultrafast chemical reactions are difficult to simulate because they involve entangled, many-body wavefunctions whose computational complexity grows rapidly with molecular size. In photochemistry, the breakdown of the Born-Oppenheimer…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…