相关论文: Sarkas: A Fast Pure-Python Molecular Dynamics Suit…

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…

This study introduces amangkurat, an open-source Python library designed for the robust numerical simulation of relativistic scalar field dynamics governed by the nonlinear Klein-Gordon equation in $(1+1)$D spacetime. The software…

Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…

Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…

The Institute for Solid State Physics (ISSP) at The University of Tokyo has been carrying out a software development project named ``the Project for Advancement of Software Usability in Materials Science (PASUMS)". Since the launch of…

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…

For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…

We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…

We present the open-source image processing software package PySAP (Python Sparse data Analysis Package) developed for the COmpressed Sensing for Magnetic resonance Imaging and Cosmology (COSMIC) project. This package provides a set of…

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…

Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics…

We present Quokka#, a versatile, open-source Python library for quantum circuit analysis. Quokka# reduces various simulation, verification, and synthesis tasks to weighted model counting (#SAT). It supports universal quantum circuits and a…

We present a flexible, open-source Python package for the accurate simulation of the $z$-propagation dynamics of ultrashort optical pulses in nonlinear waveguides, especially valid for few-cycle pulses and their interaction. The simulation…

FEniCS Mechanics is a Python package to facilitate computational mechanics simulations. The Python library dolfin, from the FEniCS Project, is used to formulate and numerically solve the problem in variational form. The general balance laws…

For the self-consistent description of various plasma sources operated in the low-pressure (nonlocal, kinetic) regime, the Particle-In-Cell simulation approach, combined with the Monte Carlo treatment of collision processes (PIC/MCC), has…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

The covariance matrix adaptation evolution strategy (CMA-ES) has been highly effective in black-box continuous optimization, as demonstrated by its success in both benchmark problems and various real-world applications. To address the need…

Manapy is a parallel, unstructured, finite-volume based solver for the solution of partial differential equations (PDE). The framework is written using Python, it is object-oriented, and is organized in such a way that it is easy to…

Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…

We present a new set of QCD codes in both message passing and data parallel versions. The message passing package used is PARMACS, although other packages may be used. Data parallel software is written in High Performance fortran, an…