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Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
The abundance and demographics of dark matter substructure is important for many areas in astrophysics and cosmological $N$-body simulations have been the primary tool used to investigate them. However, it has recently become clear that the…
Numerical MHD codes have become extraordinarily powerful tools with which to study accretion turbulence. They have been used primarily to extract values for the classical $\alpha$ parameter, and to follow complex evolutionary development.…
This paper presents an overview and introduction to Smoothed Particle Hydrodynamics and Magnetohydrodynamics in theory and in practice. Firstly, we give a basic grounding in the fundamentals of SPH, showing how the equations of motion and…
We present an algorithm for simulating the equations of ideal magnetohydrodynamics and other systems of differential equations on an unstructured set of points represented by sample particles. The particles move with the fluid, so the time…
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…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
A major trend in academia and data science is the rapid adoption of Bayesian statistics for data analysis and modeling, leading to the development of probabilistic programming languages (PPL). A PPL provides a framework that allows users to…
$clustertools$ is a Python package for analyzing star cluster simulations. The package is built around the $StarCluster$ class, which stores all data read in from the snapshot of a given model star cluster. The package contains functions…
Our aim is to study the thermal and dynamical evolution of protoplanetary disks in global simulations, including the physics of radiation transfer and magneto-hydrodynamic (MHD) turbulence caused by the magneto-rotational instability. We…
We present a new magnetohydrodynamic (MHD) simulation code with the aim of providing accurate numerical solutions to astrophysical phenomena where discontinuities, shock waves, and turbulence are inherently important. The code implements…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
We present a new software pipeline -- PyMorph -- for automated estimation of structural parameters of galaxies. Both parametric fits through a two dimensional bulge disk decomposition as well as structural parameter measurements like…
Runko is a new open-source plasma simulation framework implemented in C++ and Python. It is designed to function as an easy-to-extend general toolbox for simulating astrophysical plasmas with different theoretical and numerical models.…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
We propose a numerical method for approximate calculations of the time evolution of point particle systems given only the system's Hamiltonian function and initial conditions. The method both generates and solves the equations of motion…
We present and test a general-purpose code, called PPASPH, for evolving self-gravitating fluids in astrophysics, both with and without a collisionless component. In PPASPH, hydrodynamical properties are computed by using the SPH (Smoothed…
Automated data-driven modeling, the process of directly discovering the governing equations of a system from data, is increasingly being used across the scientific community. PySINDy is a Python package that provides tools for applying the…
Creating and maintaining computer readable geometries for use in Monte Carlo Radiation Transport (MCRT) simulations is an error-prone and time-consuming task. Simulating a system often requires geometry from different sources and modelling…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…