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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 exotic internal structure of polar topologies in multi-ferroic materials offers a rich landscape for materials science research. As the spatial scale of these entities are often sub-atomic in nature, aberration corrected transmission…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome…
Engineers and computational scientists often study the behavior of their simulations by repeated solutions with variations in their parameters, which can be for instance boundary values or initial conditions. Through such simulation…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
Effective hydrodynamic modeling is crucial for accurately predicting fluid-particle interactions in diverse fields such as biophysics and materials science. Developing and implementing hydrodynamic algorithms is challenging due to the…
QC Lab is an open-source Python package for QC dynamics simulations aimed to promote the development of QC algorithms, and their application to a wide variety of relevant model problems. It follows a modular design that facilitates…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a million particles were conducted with a massively parallel MD…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
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…
We present celmech, an open-source Python package designed to facilitate a wide variety of celestial mechanics calculations. The package allows users to formulate and integrate equations of motion incorporating user-specified terms from the…
High-fidelity computational fluid dynamics (CFD) is widely used for thermal-fluid design, but repeated CFD solves remain expensive for design optimization, uncertainty analysis, and digital-twin workflows. Recently, our team has…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Soft solids in fluids find wide range of applications in science and engineering, especially in the study of biological tissues and membranes. In this study, an Eulerian finite volume approach has been developed to simulate fully resolved…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
This paper presents a lightweight, open-source and high-performance python package for solving peridynamics problems in solid mechanics. The development of this solver is motivated by the need for fast analysis tools to achieve the large…