Related papers: Magpy: A C++ accelerated Python package for simula…

We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…

DADApy is a python software package for analysing and characterising high-dimensional data manifolds. It provides methods for estimating the intrinsic dimension and the probability density, for performing density-based clustering and for…

Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…

Lattice Boltzmann methods are a popular mesoscopic alternative to macroscopic computational fluid dynamics solvers. Many variants have been developed that vary in complexity, accuracy, and computational cost. Extensions are available to…

We present an open-source, performant, pure-python molecular dynamics (MD) suite for non-ideal plasmas. The code, Sarkas, aims to accelerate the research process by providing an MD code but also pre- and post-processing tools. Sarkas offers…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…

relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…

Multiscale modeling, which integrates material properties from ab initio calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while ab initio methods…

Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be…

Super-Droplet Method (SDM) is a probabilistic Monte-Carlo-type model of particle coagulation process, an alternative to the mean-field formulation of Smoluchowski. SDM as an algorithm has linear computational complexity with respect to the…

PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…

We present an open-source software package, Vegas, for the atomistic simulation of magnetic materials. Using the classical Heisenberg model and the Monte Carlo Metropolis algorithm, Vegas provides the required tools to simulate and analyze…

In this paper, we present MusPy, an open source Python library for symbolic music generation. MusPy provides easy-to-use tools for essential components in a music generation system, including dataset management, data I/O, data preprocessing…

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle…

Compound AI applications, which compose calls to ML models using a general-purpose programming language like Python, are widely used for a variety of user-facing tasks, from software engineering to enterprise automation, making their…

This report is concerned with the efficiency of numerical methods for simulating quantum spin systems, with the aim to implement an improved method for simulation of a time-dependent Hamiltonian that displays chirped pulses at a high…

GMP-Featurizer is a lightweight, accurate, efficient, and scalable software package for calculating the Gaussian Multipole (GMP) features \cite{GMP} for a variety of atomic systems with elements across the periodic table. Starting from the…

Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…

The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…