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BondGraphTools is a Python library for scripted modelling of complex multi-physics systems. In contrast to existing modelling solutions, BondGraphTools is based upon the well established bond graph methodology, provides a programming…

We study the problem of computing the isolated regular solutions of a system \((f_1,\ldots,f_n)\) of \(n\) polynomial equations in \(n\) variables \((X_1, \dots, X_n)\) over a field of characteristic zero \(k\). We focus on systems with a…

We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…

Partial differential equations describing the dynamics of physical systems rarely have closed-form solutions. Fourier spectral methods, which use Fast Fourier Transforms (FFTs) to approximate solutions, are a common approach to solving…

In this paper, we present pomdp_py, a general purpose Partially Observable Markov Decision Process (POMDP) library written in Python and Cython. Existing POMDP libraries often hinder accessibility and efficient prototyping due to the…

We present several topics involving the computation of dynamical systems. The emphasis is on work in progress and the presentation is informal -- there are many technical details which are not fully discussed. The topics are chosen to…

In the era of post-Moore computing, network offload emerges as a solution to two challenges: the imperative for low-latency communication and the push towards hardware specialisation. Various methods have been employed to offload protocol-…

This paper deals with the computation of polytopic invariant sets for polynomial dynamical systems. An invariant set of a dynamical system is a subset of the state space such that if the state of the system belongs to the set at a given…

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…

Many applications modeled by polynomial systems have positive dimensional solution components (e.g., the path synthesis problems for four-bar mechanisms) that are challenging to compute numerically by homotopy continuation methods. A…

The consideration of stochastic uncertainty in optimal and predictive control is a well-explored topic. Recently Polynomial Chaos Expansions (PCE) have received considerable attention for problems involving stochastically uncertain system…

In the era of big data, it is desired to develop efficient machine learning algorithms to tackle massive data challenges such as storage bottleneck, algorithmic scalability, and interpretability. In this paper, we develop a novel efficient…

PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…

Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…

The Python package fluidfft provides a common Python API for performing Fast Fourier Transforms (FFT) in sequential, in parallel and on GPU with different FFT libraries (FFTW, P3DFFT, PFFT, cuFFT). fluidfft is a comprehensive FFT framework…

With the growth of large language models, now incorporating billions of parameters, the hardware prerequisites for their training and deployment have seen a corresponding increase. Although existing tools facilitate model parallelization…

The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…

This paper discusses a Python interface for the recently published DUNE-FEM-DG module which provides highly efficient implementations of the Discontinuous Galerkin (DG) method for solving a wide range of non linear partial differential…

Flaky tests obstruct software development, and studying and proposing mitigations against them has therefore become an important focus of software engineering research. To conduct sound investigations on test flakiness, it is crucial to…

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…