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Several Monte Carlo algorithms and applications that are useful for understanding the concepts of temperature and chemical potential are discussed. We then introduce a generalization of the demon algorithm that measures the chemical…
The sensitivity analysis and validation of simulation models require specific approaches in the case of spatial models. We describe the spatialdata scala library providing such tools, including synthetic generators for urban configurations…
A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo J. Chem.…
The rapid growth of data-driven materials research has made it necessary to develop systematically designed, open databases of material properties. However, there are few open databases for polymeric materials compared to other material…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
This paper introduces PolyDiM, an open-source C++ library tailored for the development and implementation of polytopal discretization methods for partial differential equations. The library provides robust and modular tools to support…
DeeProb-kit is a unified library written in Python consisting of a collection of deep probabilistic models (DPMs) that are tractable and exact representations for the modelled probability distributions. The availability of a representative…
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,…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
Interactions between clouds and radiation are at the root of many difficulties in numerically predicting future weather and climate and in retrieving the state of the atmosphere from remote sensing observations. The large range of issues…
PyArmadillo is a linear algebra library for the Python language, with the aim of closely mirroring the programming interface of the widely used Armadillo C++ library, which in turn is deliberately similar to Matlab. PyArmadillo hence…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
We present a cross-language C++/Python program for simulations of quantum mechanical systems with the use of Quantum Monte Carlo (QMC) methods. We describe a system for which to apply QMC, the algorithms of variational Monte Carlo and…
We introduce giotto-tda, a Python library that integrates high-performance topological data analysis with machine learning via a scikit-learn-compatible API and state-of-the-art C++ implementations. The library's ability to handle various…
Kernel methods have proven to be powerful techniques for pattern analysis and machine learning (ML) in a variety of domains. However, many of their original or advanced implementations remain in Matlab. With the incredible rise and adoption…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this paper, we introduce PhotoHolmes, an open-source Python library designed to easily run and benchmark forgery detection methods on digital images. The library includes implementations of popular and state-of-the-art methods, dataset…
We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction…
The open source ALPS (Algorithms and Libraries for Physics Simulations) project provides a collection of physics libraries and applications, with a focus on simulations of lattice models and strongly correlated systems. The libraries…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…