brucefan1983 / molecular-dynamics-simulation

Sample codes for my book on molecular dynamics simulation

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

molecular-dynamics-simulation's Issues

about EMD GK

i should use this code with lammps output file,such as fix ave/correlate ？