/Molecular-Dynamics-Simulation

Sample codes for my book on molecular dynamics simulation

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

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: 887975816