Mesa 3
Mesa 3: Agent-based modeling with Python in 2025 - Published in JOSS (2025)
DART
DART: Dynamic Animation and Robotics Toolkit - Published in JOSS (2018)
cellular_raza
cellular_raza: Cellular Agent-based Modeling from a Clean Slate - Published in JOSS (2025)
simstudy
simstudy: Illuminating research methods through data generation - Published in JOSS (2020)
UXsim
UXsim: lightweight mesoscopic traffic flow simulator in pure Python - Published in JOSS (2025)
pyro
pyro: a framework for hydrodynamics explorations and prototyping - Published in JOSS (2019)
VILLASnode
VILLASnode: An Open-Source Real-time Multi-protocol Gateway - Published in JOSS (2025)
Monte Carlo / Dynamic Code (MC/DC)
Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development - Published in JOSS (2024)
EPyT
EPyT: An EPANET-Python Toolkit for Smart Water Network Simulations - Published in JOSS (2023)
PyRolL - An Extensible OpenSource Framework for Rolling Simulation
PyRolL - An Extensible OpenSource Framework for Rolling Simulation - Published in JOSS (2024)
t8code - modular adaptive mesh refinement in the exascale era
t8code - modular adaptive mesh refinement in the exascale era - Published in JOSS (2025)
EPyT-Flow
EPyT-Flow: A Toolkit for Generating Water Distribution Network Data - Published in JOSS (2024)
A Python Library for Pre- and Post-Processing of DAMASK Simulations
A Python Library for Pre- and Post-Processing of DAMASK Simulations - Published in JOSS (2025)
pyGCodeDecode
pyGCodeDecode: A Python package for time-accurate GCode simulation in material extrusion processes - Published in JOSS (2024)
UnfoldSim.jl
UnfoldSim.jl: Simulating continuous event-based time series data for EEG and beyond - Published in JOSS (2025)
TrixiParticles.jl
TrixiParticles.jl: Particle-based multiphysics simulation in Julia - Published in JOSS (2025)
DisCoTec
DisCoTec: Distributed higher-dimensional HPC simulations with the sparse grid combination technique - Published in JOSS (2025)
Adamantine 1.0
Adamantine 1.0: A Thermomechanical Simulator for Additive Manufacturing - Published in JOSS (2024)
BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
PlantSimEngine
PlantSimEngine: A Simulation Engine For The Soil-Plant-Atmosphere System - Published in JOSS (2023)
RFBzero
RFBzero: A Python package for zero-dimensional simulation of redox flow battery cycling - Published in JOSS (2024)
OpenCMP
OpenCMP: An Open-Source Computational Multiphysics Package - Published in JOSS (2022)
NLSE
NLSE: A Python package to solve the nonlinear Schrödinger equation - Published in JOSS (2024)
GridFormat
GridFormat: header-only C++-library for grid file I/O - Published in JOSS (2023)
cirq
Python framework for creating, editing, and invoking Noisy Intermediate-Scale Quantum (NISQ) circuits.
Utopia
Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems - Published in JOSS (2020)
MACE
MACE: a Machine-learning Approach to Chemistry Emulation - Published in JOSS (2025)
easyvvuq
Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.
mnt.pyfiction
An open-source design automation framework for Field-coupled Nanotechnologies
qsim
Fast C++ and Python library for state-vector simulation of quantum circuits.
simpeg
Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
amici
High-performance sensitivity analysis for large ordinary differential equation models
deltascf-aims
An application to automate core level spectroscopy simulations in FHI-aims
andes
Python toolbox / library for power system transient dynamics simulation with symbolic modeling and numerical analysis 🔥
Catalyst
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
pyiron
pyiron - an integrated development environment (IDE) for computational materials science.
pypartmc
Python (and C++) interface to PartMC with Jupyter/Python, Julia and Matlab examples
Trixi
Trixi.jl: Adaptive high-order numerical simulations of conservation laws in Julia
openfermion
Python package for compiling and analyzing quantum algorithms to simulate electronic structures.
cheetah-accelerator
Fast and differentiable particle accelerator optics simulation for reinforcement learning and optimisation applications.
mdocean
Multidisciplinary Design Optimization (MDO) to optimize an ocean wave energy converter
lindemann
lindemann is a python package to calculate the Lindemann index of a lammps trajectory
flamegpu2
FLAME GPU 2 is a GPU accelerated agent based modelling framework for CUDA C++ and Python
macpan2
Tools for building and calibrating compartmental models of infectious disease.
best-of-ps
🏆 A weekly updated ranked list of popular open-source libraries and tools for Power System Analysis.
Ciclope
Ciclope: micro Computed Tomography to Finite Elements - Published in JOSS (2023)
sinergym
Gym environment for building simulation and control using reinforcement learning
marlware
Multi-Robot Warehouse (RWARE): A multi-agent reinforcement learning environment
pydesrap_mms
Reproducible analytical pipeline (RAP) for Python discrete-event simulation (DES) implementing an M/M/s queueing model.
acces-coexsist
Learning simulation parameters from experimental data, from the micro to the macro, from laptops to clusters.
vmas
VMAS is a vectorized differentiable simulator designed for efficient Multi-Agent Reinforcement Learning benchmarking. It is comprised of a vectorized 2D physics engine written in PyTorch and a set of challenging multi-robot scenarios. Additional scenarios can be implemented through a simple and modular interface.
rdesrap_mms
Reproducible analytical pipeline (RAP) for R discrete-event simulation (DES) implementing an M/M/s queueing model.
pgmpy
Python library for building, learning, and reasoning with causal models.
reaction-network
Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (formerly at Berkeley Lab).
pysplishsplash
SPlisHSPlasH is an open-source library for the physically-based simulation of fluids.
asreview-makita
Workflow generator for simulation studies using the command line interface of ASReview LAB
stars_reproduction_template
Template repository for assessing the computational reproducibility of simulation studies on STARS
stars-reproduce-wood-2021
Assessing the computational reproducibility of Wood et al. 2021 as part of STARS.
simpa
The Simulation and Image Processing for Photonics and Acoustics (SIMPA) toolkit.
fluidx3d
The fastest and most memory efficient lattice Boltzmann CFD software, running on all GPUs and CPUs via OpenCL. Free for non-commercial use.
quantum-gates
Noisy Quantum Gates model for simulating the noise of quantum devices.
haptools
Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
snappysonic
SnappySonic is an Ultrasound Simulator for use in research and public engagement.
swirl-code
The SWIRL code is a python implementation of the "Estimated Vortex Center" (EVC) method for an automated identification of vortices in two-dimensional velocity fields.
msprime
Simulate genealogical trees and genomic sequence data using population genetic models
optical-beams-meep
Simulation of reflection and refraction of polarized opticial beams at plane and curved dielectric interfaces.
com.github.ie3-institute:PowerSystemDataModel
Provides an elaborated data model to model energy systems with a high granularity e.g. for bottom-up simulations. Additionally, useful functionalities to handle the model i/o are provided as well.
lfpykernels
Forward-model based calculations of causal spike-signal impulse response functions for finite-sized neuronal network models
ile-de-france
An open synthetic population of Île-de-France for agent-based transport simulation
icub-gazebo-grasping-sandbox
A public sandbox for simulating grasping in Gazebo with the iCub humanoid
enhancing_reaxff
Jupyter notebooks used for retraining the ReaxFF force field for the inorganic compound LiF.
simona
simona is an agent-based discrete-event power system simulation model developed @ie3-institute
myokit
Source code, issues, and discussions for Myokit: A tool for cardiac electrophysiology modelling and simulation
constrain
Control Strainer (ConStrain) is a data-driven knowledge-integrated framework that automatically verifies that building system controls function as intended.
storage-ring-gravitational-wave-observatory
Simulating the detection of millihertz (mHz) gravitational waves (GWs) from astrophysical sources by a Storage Ring Gravitational-wave Observatory (SRGO).
