Related papers: Molecular dynamics for long-range interacting syst…
In this work we propose a new numerical approach to distinguish between regular and chaotic orbits in Hamiltonian systems, based on the simultaneous integration of both the orbit and the deviation vectors using a symplectic scheme, hereby…
We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
With large-scale Integral Field Spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data.…
The graphics processing unit (GPU) has emerged as a powerful and cost effective processor for general performance computing. GPUs are capable of an order of magnitude more floating-point operations per second as compared to modern central…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
Time-reversible symplectic methods, which are precisely compatible with Liouville's phase-volume-conservation theorem, are often recommended for computational simulations of Hamiltonian mechanics. Lack of energy drift is an apparent…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
We present a novel hierarchical formulation of the fourth-order forward symplectic integrator and its numerical implementation in the GPU-accelerated direct-summation N-body code FROST. The new integrator is especially suitable for…
We investigate the performance gains from hyper-systolic implementations of n^2-loop problems on the massively parallel computer Quadrics, exploiting its 3-dimensional interprocessor connectivity. For illustration we study the communication…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
We describe an open source GPU implementation of a hybrid symplectic N-body integrator, GENGA (Gravitational ENcounters with Gpu Acceleration), designed to integrate planet and planetesimal dynamics in the late stage of planet formation and…
As high energy physics experiments reach higher luminosities and intensities, the computing burden for real time data processing and reduction grows. Following the developments in the computing landscape, multi-core processors such as…
We investigate the performance of various methods of symplectic integration, which are based on two part splitting of the integration operator, for the numerical integration of multidimensional Hamiltonian systems. We implement these…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
The LHC experiments are designed to detect large amount of physics events produced with a very high rate. Considering the future upgrades, the data acquisition rate will become even higher and new computing paradigms must be adopted for…