Related papers: A symplectic integrator for molecular dynamics on …
Symplectic integrator plays a pivotal role in the long-term tracking of charged particles within accelerators. To get symplectic maps in accurate simulation of single-particle trajectories, two key components are addressed: precise…
We present a simple quantum mechanical model describing excited rotational states of molecules in superfluid helium nanodroplets, as recently studied in non-adiabatic molecular alignment experiments [Cherepanov et al., Phys. Rev. A 104,…
Most numerical integration algorithms are not designed specifically for Hamiltonian systems and do not respect their characteristic properties, which include the preservation of phase space volume with time. This can lead to spurious…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
In order to perform numerical studies of long-term stability in nonlinear Hamiltonian systems, one needs a numerical integration algorithm which is symplectic. Further, this algorithm should be fast and accurate. In this paper, we propose…
We consider the numerical integration of the matrix Hill's equation. Parametric resonances can appear and this property is of great interest in many different physical applications. Usually, the Hill's equations originate from a Hamiltonian…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
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…
Dependable numerical results from long-time simulations require stable numerical integration schemes. For Hamiltonian systems, this is achieved with symplectic integrators, which conserve the symplectic condition and exactly solve for the…
Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh--Benard convection at the discrete-particle level. Two examples are considered, one in which an almost perfect array of hexagonally-shaped…
Molecular dynamics simulations yield large amounts of trajectory data. For their durable storage and accessibility an efficient compression algorithm is paramount. State of the art domain-specific algorithms combine quantization, Huffman…
We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…
With the approach of exascale computing era, particle-based models are becoming the focus of research due to their excellent scalability. We present a new code, Slurm, which implements the classic particle-in-cell algorithm for modeling…
We consider two strongly hyperbolic Hamiltonian formulations of general relativity and their numerical integration with a free and a partially constrained symplectic integrator. In those formulations we use hyperbolic drivers for the shift…
Methods for building a consistent interface between hydrodynamic and simulation modules is presented. These methods account for the backflow across the hydrodynamic/simulation hyper-surface. The algorithms are efficient, relatively…
Direct N-body simulations and symplectic integrators are effective tools to study the long-term evolution of planetary systems. The Wisdom-Holman (WH) integrator in particular has been used extensively in planetary dynamics as it allows for…
We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics…
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…