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KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily…
PYROBOCOP is a lightweight Python-based package for control and optimization of robotic systems described by nonlinear Differential Algebraic Equations (DAEs). In particular, the package can handle systems with contacts that are described…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
We present here our ongoing work on a Domain Specific Language which aims to simplify Monte-Carlo simulations and measurements in the domain of Lattice Quantum Chromodynamics. The tool-chain, called Qiral, is used to produce…
Aggregate programming is a field-based coordination paradigm with over a decade of exploration and successful applications across domains including sensor networks, robotics, and IoT, with implementations in various programming languages,…
partycls is a Python framework for cluster analysis of systems of interacting particles. By grouping particles that share similar structural or dynamical properties, partycls enables rapid and unsupervised exploration of the system's…
This paper describes the VARTOOLS program, which is an open-source command-line utility, written in C, for analyzing astronomical time-series data, especially light curves. The program provides a general-purpose set of tools for processing…
Mathematical models allow us to gain a deeper understanding of real-world dynamical systems. One of the most powerful mathematical frameworks for modeling real-world phenomena are systems of differential equations. In the majority of fields…
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's…
In recent years, the number of hybrid algorithms that combine quantum and classical computations has been continuously increasing. These two approaches to computing can mutually enhance each others' performances thus bringing the promise of…
The $\texttt{torch-choice}$ is an open-source library for flexible, fast choice modeling with Python and PyTorch. $\texttt{torch-choice}$ provides a $\texttt{ChoiceDataset}$ data structure to manage databases flexibly and…
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…
pyspeckit is a toolkit and library for spectroscopic analysis in Python. We describe the pyspeckit package and highlight some of its capabilities, such as interactively fitting a model to data, akin to the historically widely-used splot…
Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in…
The multi-GPU open-source package QCDGPU for lattice Monte Carlo simulations of pure SU(N) gluodynamics in external magnetic field at finite temperature and O(N) model is developed. The code is implemented in OpenCL, tested on AMD and…
Temporal logic is an important tool for specifying complex behaviors of systems. It can be used to define properties for verification and monitoring, as well as goals for synthesis tools, allowing users to specify rich missions and tasks.…
Cardiac electrophysiology (CEP) simulations are increasingly used for understanding cardiac arrhythmias and guiding clinical decisions. However, these simulations typically require high-performance computing resources with numerous CPU…
An open-source, Python-based Temporal Analysis of Products (TAP) reactor simulation and processing program is introduced. TAPsolver utilizes algorithmic differentiation for the calculation of highly accurate derivatives, which are used to…
Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
The Object Constraint Language (OCL) has been widely used in the modeling community to complement software models for precisely defining constraints and business rules for the modeled systems. There is a limited number of tools supporting…