相关论文: Sarkas: A Fast Pure-Python Molecular Dynamics Suit…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
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…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
Computational materials science produces large quantities of data, both in terms of high-throughput calculations and individual studies. Extracting knowledge from this large and heterogeneous pool of data is challenging due to the wide…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
PyBADS is a Python implementation of the Bayesian Adaptive Direct Search (BADS) algorithm for fast and robust black-box optimization (Acerbi and Ma 2017). BADS is an optimization algorithm designed to efficiently solve difficult…
Modified Newtonian dynamics (MOND) is a promising alternative to dark matter. To further test the theory, there is a need for fluid- and particle-dynamics simulations. The force in MOND is not a direct particle-particle interaction, but…
Magpy is a C++ accelerated Python package for modelling and simulating the magnetic dynamics of nano-sized particles. Nanoparticles are modelled as a system of three-dimensional macrospins and simulated with a set of coupled stochastic…
Python is a particularly appealing language to carry out data analysis, owing in part to its user-friendly character as well as its access to well maintained and powerful libraries like NumPy and SciPy. Still, for the purpose of analyzing…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. During molecular dynamics simulations, data…
An open source software package for performing dynamic RMS simulation of small to medium-sized power systems is presented, written entirely in the Python programming language. The main objective is to facilitate fast prototyping of new wide…
We present PySCo, a fast and user-friendly Python library designed to run cosmological $N$-body simulations across various cosmological models, such as $\Lambda$CDM and $w_0w_a$CDM, and alternative theories of gravity, including $f(R)$,…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
pPython seeks to provide a parallel capability that provides good speed-up without sacrificing the ease of programming in Python by implementing partitioned global array semantics (PGAS) on top of a simple file-based messaging library…
Direct Numerical Simulations (DNS) of the Navier Stokes equations is an invaluable research tool in fluid dynamics. Still, there are few publicly available research codes and, due to the heavy number crunching implied, available codes are…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…