Related papers: SEAMM: A Simulation Environment for Atomistic and …
This paper summarizes the development of Veamy, an object-oriented C++ library for the virtual element method (VEM) on general polygonal meshes, whose modular design is focused on its extensibility. The linear elastostatic and Poisson…
Nowadays electrical impedance spectroscopy (EIS) has become an advanced experimental technique with a wide range of applications: from simple passive circuits diagnostics to semiconductor high-end device development and breakthrough…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
This paper delivers a software -- libEMM -- for 3D controlled-source electromagnetics (CSEM) modelling in fictitious wave domain, based on the newly developed high-order finite-difference time-domain (FDTD) method on non-uniform grid. The…
Earth system models (ESMs), which simulate the physics and chemistry of the global atmosphere, land, and ocean, are often used to generate future projections of climate change scenarios. These models are far too computationally intensive to…
ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and…
The Transfer Matrix Method (TMM) has become a prominent tool for the optical simulation of thin$-$film solar cells, particularly among researchers specializing in organic semiconductors and perovskite materials. As the commercial viability…
PESummary is a Python software package for processing and visualising data from any parameter estimation code. The easy to use Python executable scripts and extensive online documentation has resulted in PESummary becoming a key component…
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…
CMasher is a Python package that provides a curated collection of scientific colormaps, showcased in the online documentation (https://cmasher.readthedocs.io). The colormaps in CMasher are all designed to be perceptually uniform sequential…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
Simulation ensembles are a common tool in physics for understanding how a model outcome depends on input parameters. We analyze an active particle system, where each particle can use energy from its surroundings to propel itself. A…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
The Imaging Computational Microscope (ICM) is a suite of computational tools for automated analysis of functional imaging data that runs under the cross-platform MATLAB environment (The Mathworks, Inc.). ICM uses a semi-supervised…
We present an XML-based simulation authoring environment. The proposed description language allows to describe mathematical objects such as systems of ordinary differential equations, partial differential equations in two dimensions, or…
Organizations have realized the importance of data analysis and its benefits. This in combination with Machine Learning algorithms has allowed to solve problems more easily, making these processes less time-consuming. Neural networks are…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the…
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…
Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited…