Related papers: atoMEC: An open-source average-atom Python code
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Atomic-scale phase-field modeling formulates the probability densities of atomic vibrations as Gaussian distributions and derives a free energy functional using variational Gaussian theory and interatomic potentials. This framework permits…
We have built an integrated computational platform for material properties at extreme conditions, ProME (Professional Materials at Extremes) v1.0, which enables integrated calculations for multicomponent alloys, covering high temperatures…
The Combustion Toolbox (CT) is a newly developed open-source thermochemical code designed to solve problems involving chemical equilibrium for both gas- and condensed-phase species. The kernel of the code is based on the theoretical…
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be…
QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron-electron interactions using various approximate master equation approaches. The package provides a framework for…
We analyze the circumgalactic medium (CGM) for eight commonly-used cosmological codes in the AGORA collaboration. The codes are calibrated to use identical initial conditions, cosmology, heating and cooling, and star formation thresholds,…
Existing abstract models of quantum computation make reference to circuit elements, much in contrast to their classical counterparts. Circuits, as a model of computation, substantially limit algorithmic expression and obscure high-level…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Consensus is a common method for computing a function of the data distributed among the nodes of a network. Of particular interest is distributed average consensus, whereby the nodes iteratively compute the sample average of the data stored…
Pseudo-Boolean constraints, also known as 0-1 Integer Linear Constraints, are used to model many real-world problems. A common approach to solve these constraints is to encode them into a SAT formula. The runtime of the SAT solver on such…
Large models have achieved remarkable performance across various tasks, yet they incur significant computational costs and privacy concerns during both training and inference. Distributed deployment has emerged as a potential solution, but…
Due to the high dimensionality or multimodality that is common in modern astronomy, sampling Bayesian posteriors can be challenging. Several publicly available codes based on different sampling algorithms can solve these complex models, but…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
The large amount of spectra obtained during the epoch of extensive spectroscopic surveys of Galactic stars needs the development of automatic procedures to derive their atmospheric parameters and individual element abundances. Starting from…
Developing large-scale foundational datasets is a critical milestone in advancing artificial intelligence (AI)-driven scientific innovation. However, unlike AI-mature fields such as natural language processing, materials science,…
We present an open-source computer program written in Python language for quantum measurement and related issues. In our program, quantum states and operators, including quantum gates, can be developed into a quantum-object function…
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…
Models of complicated systems can be represented in different ways - in scientific papers, they are represented using natural language text as well as equations. But to be of real use, they must also be implemented as software, thus making…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…