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BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of PDEs, but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been…
We present a highly efficient molecular dynamics scheme for calculating the concentration depth profile of dopants in ion irradiated materials. The scheme incorporates several methods for reducing the computational overhead, plus a rare…
The Software Transactional Memory (STM) model is an original approach for controlling concurrent accesses to ressources without the need for explicit lock-based synchronization mechanisms. A key feature of STM is to provide a way to group…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
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…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Molecular dynamics (MD) simulations involving reactive potentials can be used to model material failure. The empirical potentials which are used in such simulations are able to adapt to the atomic environment, at the expense of a…
We extend the rigorous adiabatic coupled-channel formalism to ultracold nonreactive atom-molecule collisions in the presence of an external magnetic field. The wavefunction of the collision complex is expanded in adiabatic basis states…
In this article we present a new formulation and an associated algorithm for the simultaneous numerical simulation of multiple condensed phase explosives in direct contact with each other, which may also be confined by (or interacting with…
Computational modeling is an important aspect of the research on nuclear waste materials. In particular, atomistic simulations, when used complementary to experimental efforts, contribute to the scientific basis of safety case for nuclear…
Encoding a dimension in the internal degree of freedom of an atom provides an interesting tool for quantum simulation, facilitating the realization of artificial gauge fields. We propose an extension of the synthetic dimension toolbox,…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Recent increases in supercomputing power, driven by the multi-core revolution and accelerators such as the IBM Cell processor, graphics processing units (GPUs) and Intel's Many Integrated Core (MIC) technology have enabled kinetic…
Metal coordination is ubiquitous in Nature and central in many applications ranging from nanotechnology to catalysis and environmental chemistry. Complex formation results from the subtle interplay between different thermodynamic, kinetic,…
Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required…
There are many astrophysical and laboratory scenarios where kinetic effects play an important role. These range from astrophysical shocks and plasma shell collisions, to high intensity laser-plasma interactions, with applications to fast…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…