Assessment and optimization of the fast inertial relaxation engine (FIRE) for energy minimization in atomistic simulations and its implementation in LAMMPS

Coarse-Grained Simulation of DNA using LAMMPS

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-…

LAMMPS模拟软件包教程集

A Set of Tutorials for the LAMMPS Simulation Package

针对LAMMPS分子模拟软件初学者上手难的问题，本文推出包含8篇基础与进阶教程的教程集，并配套专用的LAMMPS-GUI工具，降低新用户的学习门槛。

Mechanical Properties of Schwarzites - A Fully Atomistic Reactive Molecular Dynamics Investigation

Schwarzites are crystalline, 3D porous structures with stable negative curvature formed of sp2-hybridized carbon atoms. These structures present topologies with tunable porous size and shape and unusual mechanical properties. In this work, we have investigated the mechanical behavior under compressive strains and energy absorption of four different Schwarzites, through reactive molecular dynamics simulations, using the ReaxFF force field as available in the LAMMPS code. We considered two Schwarzites families, the so-called Gyroid and Primitive and two structures from each family. Our results a…

自适应精度势用于大规模原子模拟

Adaptive-precision potentials for large-scale atomistic simulations

本研究提出一种结合传统势与机器学习势的自适应精度方法，通过逐原子局部结构分析动态调整精度，在LAMMPS中实现大规模原子模拟，以铜为例获得11.3倍加速且保持高精度。

材料科学中自适应精度原子间势的负载均衡

Load balancing for adaptive-precision interatomic potentials in materials science

针对自适应精度原子间势模拟，比较LAMMPS与ALL库的负载均衡方法，ALL修正张量法将不平衡因子从3.0降至1.7，并提出理想负载均衡频率策略。

ELECTRODE: An electrochemistry package for atomistic simulations

Constant potential methods (CPM) enable computationally efficient simulations of the solid-liquid interface at conducting electrodes in molecular dynamics (MD). They have been successfully used, for example, to realistically model the behavior of ionic liquids or water-in-salt electrolytes in supercapacitors and batteries. The CPM models conductive electrodes by updating charges of individual electrode atoms according to the applied electric potential and the (time-dependent) local electrolyte structure. Here we present a feature-rich CPM implementation, called ELECTRODE, for the Large-scale A…