Related papers: Sesame: a 2-dimensional solar cell modeling tool
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…
The context of this work is the design of a software, called MEMSALab, dedicated to the automatic derivation of multiscale models of arrays of micro- and nanosystems. In this domain a model is a partial differential equation. Multiscale…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
OpenSesame is a program for generating tabular equations of state (EOS), with capabilities for multiphase EOS construction. In this tutorial, we provide an overview of how to run OpenSesame to construct a multiphase EOS. We discuss some…
This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…
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…
Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be…
We present GLEAM (Galaxy Line Emission & Absorption Modeling), a Python tool for fitting Gaussian models to emission and absorption lines in large samples of 1D extragalactic spectra. GLEAM is tailored to work well in batch mode without…
In many-particle problems involving interacting fermions or bosons, the most natural language for expressing the Hamiltonian, the observables, and the basis states is the language of the second-quantization operators. It thus appears…
Complete Feynman diagram automatic computation systems are now coming of age after many years of development. They are made available to the high energy physics community through user-friendly interfaces. Theorists and experimentalists can…
Correct performance assessment is crucial for evaluating modern artificial intelligence algorithms in medicine like deep-learning based medical image segmentation models. However, there is no universal metric library in Python for…
This paper summarizes the development of mVEM, a MATLAB software package containing efficient and easy-following codes for various virtual element methods (VEMs) published in the literature. We explain in detail the numerical implementation…
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…
SPSMAT (Spectral/Pseudospectral matrix method) is an add-on for Octave, that helps you solve nonfractional-/fractional ordinary/partial differential/integral equations. In this version, as the first version, the well-defined spectral or…
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…
We introduce QuiverTools, a new software package, available in both a SageMath and Julia version, to study quivers and their moduli spaces of representations. Its key features are the computation of general subdimension vectors, leading to…
pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are…
We have developed an open-source software package (SedSimple) for stratigraphic forward modeling. It is aimed for use in research and education. The package uses ASCII files for input and output to facilitate understanding, debugging and…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…