Related papers: Magpy: A C++ accelerated Python package for simula…
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…
Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…
We present NeuralMag, a flexible and high-performance open-source Python library for micromagnetic simulations. NeuralMag leverages modern machine learning frameworks, such as PyTorch and JAX, to perform efficient tensor operations on…
We present the AGATE simulation code, a Python-based framework developed primarily for solving the magnetohydrodynamics (MHD) equations while maintaining adaptability to other equation sets. The code employs a modular, object-oriented…
We present the public release of EXP, a basis function expansion C++ library and Python package for running N-body galactic simulations and dynamical discovery. EXP grew out of the need for methodology that seamlessly connects theoretical…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Scipp is heavily inspired by the Python library xarray. It enriches raw NumPy-like multi-dimensional arrays of data by adding named dimensions and associated coordinates. Multiple arrays are combined into datasets. On top of this, scipp…
MARTY is a C++ computer algebra system specialized for High Energy Physics that can calculate amplitudes, squared amplitudes and Wilson coefficients in a large variety of beyond the Standard Model scenarios up to the one-loop order. It is…
This is the user manual for CosmoLattice, a modern package for lattice simulations of the dynamics of interacting scalar and gauge fields in an expanding universe. CosmoLattice incorporates a series of features that makes it very versatile…
We present our open-source Python module Commics for the study of the magnetization dynamics in ferromagnetic materials via micromagnetic simulations. It implements state-of-the-art unconditionally convergent finite element methods for the…
In this article, we present Gammapy, an open-source Python package for the analysis of astronomical $\gamma$-ray data, and illustrate the functionalities of its first long-term-support release, version 1.0. Built on the modern Python…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
FEniCS Mechanics is a Python package to facilitate computational mechanics simulations. The Python library dolfin, from the FEniCS Project, is used to formulate and numerically solve the problem in variational form. The general balance laws…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
NEMESISPY is a Python package developed to perform parametric atmospheric modelling and radiative transfer calculation for the retrievals of exoplanetary spectra. It is a recent development of the well-established Fortran NEMESIS library…
We develop the Mechanic package, which is a new numerical framework for dynamical astronomy. The aim of our software is to help in massive numerical simulations by efficient task management and unified data storage. The code is built on top…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
magnum.np is a micromagnetic finite-difference library completely based on the tensor library PyTorch. The use of such a high level library leads to a highly maintainable and extensible code base which is the ideal candidate for the…