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We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general…
GEANT4 is a particle physics simulation tool used to develop and optimize radiation detectors. While C++ based examples exist, Python's growing popularity necessitates the development of a more accessible Python bindings interface. This…
In this paper, we introduce OWLAPY, a comprehensive Python framework for OWL ontology engineering. OWLAPY streamlines the creation, modification, and serialization of OWL 2 ontologies. It uniquely integrates native Python-based reasoners…
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 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…
We demonstrate that a small transformer can learn to execute programs in MicroPy, a simplified yet computationally universal programming language. Given procedure definitions together with an expression to evaluate, the transformer predicts…
High-energy physics phenomenology often requires linking multiple computational tools to evaluate observables, likelihoods, and experimental constraints across nontrivial parameter spaces. In this work, we introduce Jarvis-HEP, a…
radioactivedecay is a Python package for radioactive decay modelling. It contains functions to fetch decay data, define inventories of nuclides and perform decay calculations. The default nuclear decay dataset supplied with radioactivedecay…
Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have aided multiple fields including chemistry, biology and physics. However, accurate quantum dynamical simulations based on model…
Condensed matter compounds typically form crystals, which break the rotational and translational invariance of space but remain invariant under a discrete set of symmetry operations. Understanding the effects allowed by this symmetry…
ABCpy is a highly modular scientific library for Approximate Bayesian Computation (ABC) written in Python. The main contribution of this paper is to document a software engineering effort that enables domain scientists to easily apply ABC…
The limited distinctness of physical systems is roughly expressed by uncertainty relations. Here we show distinctness is a finite resource we can exactly count to define basic physical quantities, limits to the resolution of space and time,…
diffpy$.$morph addresses a need to gain scientific insights from 1D scientific spectra in model independent ways. A powerful approach for this is to take differences between pairs of spectra and look for meaningful changes that might…
This paper presents SunPy (version 0.5), a community-developed Python package for solar physics. Python, a free, cross-platform, general-purpose, high-level programming language, has seen widespread adoption among the scientific community,…
A simple procedure for restoring the constants in physical equations is introduced by a consistent consideration of the correspondence between the symbols representing physical quantities and pairs formed by numerical values and unit…
This paper discusses the design and implementation of a Python-based toolset to aid in assessing the response of the UK's Advanced Gas Reactor nuclear power stations to earthquakes. The seismic analyses themselves are carried out with a…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…
Programmers may be hesitant to use declarative systems, because of the associated learning curve. In this paper, we present an API that integrates the IDP Knowledge Base system into the Python programming language. IDP is a state-of-the-art…
Understanding the interactions between atoms and light is at the heart of atomic physics. Being able to `experiment' with various system parameters, produce plots of the results and interpret these is very useful, especially for those new…