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preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics simulations by gluing together separate software packages. This paper summarizes the development efforts in preCICE of the past five years. During…
The absorption and emission of light by exoplanet atmospheres encode details of atmospheric composition, temperature, and dynamics. Fundamentally, simulating these processes requires detailed knowledge of the opacity of gases within an…
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
Chiplet architectures are on the rise as they promise to overcome the scaling challenges of monolithic chips. A key component of such architectures is an efficient inter-chiplet interconnect (ICI). The ICI design space is huge as there are…
Scikit-network is a Python package inspired by scikit-learn for the analysis of large graphs. Graphs are represented by their adjacency matrix in the sparse CSR format of SciPy. The package provides state-of-the-art algorithms for ranking,…
RISC-V is an extendable Instruction Set Architecture, growing in popularity for embedded systems. However, optimizing it to specific requirements, imposes a great deal of manual effort. To bridge the gap between software and ISA, the tool…
Nexus-CAT (Cluster Analysis Toolkit) is an open-source Python package for cluster detection and percolation analysis of atomistic simulation trajectories. Standard structural tools, such as the pair distribution function or structure…
A number of new functionalities have been added to the Alloy Theoretic Automated Toolkit (ATAT) since it was last reviewed in this journal in 2002. ATAT can now handle multicomponent multisublattice alloy systems, nonconfigurational sources…
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. This search has stimulated the development of several cloud platforms that abstract the complexity of…
We present the novel, semi-automated clustering tool ASPECT for analysing voluminous archives of spectra. The heart of the program is a neural network in form of Kohonen's self-organizing map. The resulting map is designed as an icon map…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
We present srlearn, a Python library for boosted statistical relational models. We adapt the scikit-learn interface to this setting and provide examples for how this can be used to express learning and inference problems.
\textsc{Pykat} is a Python package which extends the popular optical interferometer modelling software \textsc{Finesse}. It provides a more modern and efficient user interface for conducting complex numerical simulations, as well as…
We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…
The eT program is an open source electronic structure package with emphasis on coupled cluster and multilevel methods. It includes efficient spin adapted implementations of ground and excited singlet states, as well as equation of motion…
Performance assessment is a key issue in the process of proposing new machine learning/statistical estimators. A possible method to complete such task is by using simulation studies, which can be defined as the procedure of estimating and…
DESlib is an open-source python library providing the implementation of several dynamic selection techniques. The library is divided into three modules: (i) \emph{dcs}, containing the implementation of dynamic classifier selection methods…
The upcoming exascale era will push the changes in computing architecture from classical CPU-based systems in hybrid GPU-heavy systems with much higher levels of complexity. While such clusters are expected to improve the performance of…
The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet…