Related papers: dlmontepython: A Python library for automation and…
DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation.…
Machine learning solutions are very popular in the field of chemoinformatics, where they have numerous applications, such as novel drug discovery or molecular property prediction. Molecular fingerprints are algorithms commonly used for…
ParaMonte::Python (standing for Parallel Monte Carlo in Python) is a serial and MPI-parallelized library of (Markov Chain) Monte Carlo (MCMC) routines for sampling mathematical objective functions, in particular, the posterior distributions…
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…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Computational models can provide significant insight into the operation mechanisms and deficiencies of photovoltaic solar cells. Solcore is a modular set of computational tools, written in Python 3, for the design and simulation of…
Creating and maintaining computer readable geometries for use in Monte Carlo Radiation Transport (MCRT) simulations is an error-prone and time-consuming task. Simulating a system often requires geometry from different sources and modelling…
Monte Carlo (MC) simulations of lattice models are a widely used way to compute thermodynamic properties of substitutional alloys. A limitation to their more widespread use is the difficulty of driving a MC simulation in order to obtain the…
We present a modular analysis program written in Python devoted to the estimation of autocorrelation times for Monte Carlo simulations by means of the $\Gamma$-method algorithm. We give a brief review of this method and describe the main…
This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…
Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective…
The role of data libraries in Monte Carlo simulation is discussed. A number of data libraries currently in preparation are reviewed; their data are critically examined with respect to the state-of-the-art in the respective fields. Extensive…
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 electron systems. The…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating…
mlpy is a Python Open Source Machine Learning library built on top of NumPy/SciPy and the GNU Scientific Libraries. mlpy provides a wide range of state-of-the-art machine learning methods for supervised and unsupervised problems and it is…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
M-estimation is a general statistical framework that simplifies estimation. Here, we introduce delicatessen, a Python library that automates the tedious calculations of M-estimation, and supports both built-in user-specified estimating…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python…