Related papers: OpenMM-Python-Force: Deploying Accelerated Python …

Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…

Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…

We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands…

The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the according X-ray scattering response in one-dimensional sample structures.…

An improved implementation of an N-body code for simulating collisionless cosmological dynamics is presented. TPM (Tree-Particle-Mesh) combines the PM method on large scales with a tree code to handle particle-particle interactions at small…

This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…

We present mrfmsim, an open-source Python package that facilitates the design, simulation, and analysis of magnetic resonance force microscopy (MRFM) experiments. MRFM is a scanning-probe technique that detects magnetic resonance from…

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…

This paper puts forward the vision of creating a library of neural-network-based models for power system simulations. Traditional numerical solvers struggle with the growing complexity of modern power systems, necessitating faster and more…

Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…

Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in the TorchMD-Net software, a pivotal…

In this paper we use Python to implement two efficient modular exponentiation methods: the adaptive m-ary method and the adaptive sliding-window method of window size k, where both m's are adaptively chosen based on the length of exponent.…

The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…

Synchrotron processes, the radiative processes associated with the interaction of energetic charged particles with magnetic field, are of interest in many areas in astronomy, from the interstellar medium to extreme environments near compact…

Scientific foundation models hold great promise for advancing nuclear and particle physics by improving analysis precision and accelerating discovery. Yet, progress in this field is often limited by the lack of openly available large scale…

Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States…

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…

In the field of computational fluid dynamics, direct numerical simulations generate highly detailed data for the analysis of turbulent flows by resolving all relevant physical scales. Yet their large size, complexity, and heterogeneity make…

Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit. Here, we present a review of the…