brucefan1983/Molecular-Dynamics-Simulation：我的分子动力学模拟书籍的示例代码

brucefan1983

项目介绍

brucefan1983/Molecular-Dynamics-Simulation 是一个托管在 GitHub 上的开源项目，主要使用 Jupyter Notebook 编写，采用 GNU General Public License v3.0 许可证，目前获得 297 个 Star、65 次 Fork。

仓库全名: brucefan1983/Molecular-Dynamics-Simulation

README 摘要

Supporting materials for my on-going book Molecular dynamics simulation Source code and examples in the book Chapter | Language/software | Description | Author | Discussed in the book? | :---------------|:---------------|:---------------|:---------------|:-------------| 1 Classical Physics | Python | Demonstrating the velocity-Verlet integrator in terms of 1D harmonic oscillator | Ke Xu | Yes | 2 Simple molecular…

完整内容见 GitHub 原始 README 或本页。

常见问题

Molecular-Dynamics-Simulation 用什么语言开发？

主要使用 Jupyter Notebook 编写，采用 GNU General Public License v3.0 许可证，目前有 297 个 Star。

Molecular-Dynamics-Simulation 可以免费商用吗？

仓库标注的许可证为 GNU General Public License v3.0，商用前请先阅读仓库 LICENSE 文件确认授权范围。

如何获取 Molecular-Dynamics-Simulation 的源码？

可以直接克隆仓库：git clone https://github.com/brucefan1983/Molecular-Dynamics-Simulation.git，默认分支为 master；安装与运行步骤见仓库 README。

Molecular-Dynamics-Simulation 最近还在维护吗？

仓库最近一次更新为 1月26日，当前没有未关闭的 Issue；Star 数为 297，可作为社区活跃度的参考。

关于

GitHub 原始描述（英文）

Sample codes for my book on molecular dynamics simulation

molecular-dynamics molecular-dynamics-simulation

GNU General Public License v3.0
297 Stars
65 Forks
10 Watching

描述取自 GitHub 官方 API，保持仓库作者书写的原文。

简要分析

热度分

437

价值分

198

活跃状态

活跃

GitHub

语言占比

C++

Jupyter Notebook

MATLAB

Python

贡献者

Supporting materials for my on-going book Molecular dynamics simulation

Source code and examples in the book

Chapter	Language/software	Description	Author	Discussed in the book?
1 Classical Physics	Python	Demonstrating the velocity-Verlet integrator in terms of 1D harmonic oscillator	Ke Xu	Yes
2 Simple molecular dynamics	C++	A simple MD code without using neighbor list	Zheyong Fan	Yes
3 Simulation box and neighbor list	C++	A linear-scaling MD code using neighbor list	Zheyong Fan	Yes
4 Empirical potentials	C++	Implemenation and validation of the Tersoff potential	Zheyong Fan	Yes
	GPUMD	Cross-validate the Tersoff potential between GPUMD and standalone C++	Zheyong Fan	Yes
5 Machine-learned potentials	GPUMD	Train a NEP model for silicon crystal	Zheyong Fan	Yes
6 Thermostatting methods	Python	Implementating the Nose-Hoover thermostat in terms of 1D harmonic oscillator	Shuning Pan	Yes
	Python	Implementating the Nose-Hoover chain thermostat in terms of 1D harmonic oscillator	Shuning Pan	Yes
	Python	Implementating the Langevin thermostat in terms of 1D harmonic oscillator	Shuning Pan	Yes
	GPUMD	Comparing the thermostats in GPUMD	Zheyong Fan	Yes
7 Barostatting methods	GPUMD	Demonstrating the usage of the barostatting methods in GPUMD	Zheyong Fan	Yes
	GPUMD	Comparing the barostats in GPUMD	Zheyong Fan	Yes
8 Static properties	GPUMD	Demonstrating statistical error	Zheyong Fan	Yes
	GPUMD	Demonstrating the study of thermal expansion using GPUMD	Zheyong Fan	Yes
	GPUMD	Demonstrating the calculation of RDF of water in GPUMD	Zekun Chen	Yes
	Python	Calculating RDF from saved trajectory	Nan Xu	Yes
9 Transport properties	GPUMD	Calculating self diffusion coefficient of liquid silicon using GPUMD and NEP	Zheyong Fan	Yes
	GPUMD	Calculating viscosity of liquid silicon using GPUMD and NEP	Zheyong Fan	Yes
	GPUMD	Calculating thermal transport properties of crystalline silicon using GPUMD and NEP	Zheyong Fan	Yes
	C++	Standalone MD code calculating self diffusion coefficient	Zheyong Fan	No
	C++	Standalone MD code calculating thermal conductivity using EMD	Zheyong Fan	No
	C++	Standalone MD code calculating thermal conductivity using HNEMD	Zheyong Fan	No
10 Path-integral molecular dynamics	GPUMD	Calculating the radial distribution function of water using GPUMD and NEP	Zekun Chen	Yes
	Python	A full PIMD code in terms of 1D harmonic oscillator	Nan Xu	Yes

Discussion group for the book

QQ group: 778083814

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Molecular-Dynamics-Simulation