相关论文: Sarkas: A Fast Pure-Python Molecular Dynamics Suit…
The dynamic mode decomposition (DMD) is a simple and powerful data-driven modeling technique that is capable of revealing coherent spatiotemporal patterns from data. The method's linear algebra-based formulation additionally allows for a…
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…
We describe Rabacus, a Python package for calculating the transfer of hydrogen ionizing radiation in simplified geometries relevant to astronomy and cosmology. We present example solutions for three specific cases: 1) a semi-infinite slab…
Stokesian Dynamics (SD) is a powerful computational framework for simulating the motion of particles in a viscous Newtonian fluid under Stokes-flow conditions. Traditional SD implementations can be computationally expensive as they rely on…
We present the first open-source, GPU-based code for complex plasmas. The code, OpenDust, aims to provide researchers both experimenters and theorists user-friendly and high-performance tool for self-consistent calculation forces, acting on…
The acceleration of material property calculations while maintaining ab initio accuracy (1 meV/atom) is one of the major challenges in computational physics. In this paper, we introduce a Python package enhancing the computation of (finite…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
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…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
We present MADLens a python package for producing non-Gaussian lensing convergence maps at arbitrary source redshifts with unprecedented precision. MADLens is designed to achieve high accuracy while keeping computational costs as low as…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
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…
The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
The advancement of machine learning and the availability of large-scale reaction datasets have accelerated the development of data-driven models for computer-aided synthesis planning (CASP) in the past decade. Here, we detail the newest…
We present SymForce, a library for fast symbolic computation, code generation, and nonlinear optimization for robotics applications like computer vision, motion planning, and controls. SymForce combines the development speed and flexibility…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
Runko is a new open-source plasma simulation framework implemented in C++ and Python. It is designed to function as an easy-to-extend general toolbox for simulating astrophysical plasmas with different theoretical and numerical models.…