5. Molecular Dynamics¶

Radiation Damage Simulations with Molecular Dynamics

Before introducing the simulation,many people may think why we need simulations,what can we do through simulations

5.1. Basic Concepts and Methods¶

Molecular dynamics simulations compute the motions of individual molecules in models of solids,liquids and gases and it is a technique that allows a numerical “thought experiment” to be carried out using a model that,to a limited extent,approximates a real physical or chemical system.Such a “virtual laboratory” approach has the advantage that many such “experiments” can be easily set up and carried out in succession by simply varying the control parameters.Morever,extreme conditions,such high temperature and obvious downside is that the results are only as good as the numerical model.In addition,the results can be artificially biased if the molecular dynamics calculation is unable to sample an adequate number of microstates over the time it is allowed to run.

5.2. Lammps Tutortials¶

LAMMPS is a classical molecular dynamics(MD) code that models ensembles of particles in a liquid,solid,or gaseous state.It can model atomic,polymeric,biological,solid-state(metals,ceramics,oxides),granular,coarse-grained,or macroscopic systems using a variety of interatomic potentials(force fields) and boundary conditions.It can model 2d or 3d systems with only a few particles up to millions or billions.

5.2.1. Install LAMMPS¶

In this section,I will show you the most direct method to compile and buid the parallel lammps in you Linux(Ubuntu) system. Before install the lammps,you should install the MPICH and FFTW in your PC machine.

5.2.1.1. Prerequisites¶

Note

MPICH should be installed firstly

Before you install the mpich,you should execute the following command in order to meet some of the dependencies:

sudo apt install gfortran
sudo apt install gcc
sudo apt install g++

Then you can go to it’s source website and download the package,like mpich-3.3.1.tar.gz,when you unzip the package,read the README file,you can can implement the following commands:

tar -zxvf mpich-3.3.1.tar.gz
cd mpich-3.2
./configure --prefix=/home/day/computer/mpich3/( = you should remmember this path)
make & make install

Okay you have install the mpich in your system,next you should configure enviroment

cd ~
vim .bashrc

In the .bashrc file,add the following statements

export PATH=/home/day/computer/mpich3/bin:$PATH
export MANPATH=//home/day/computer/mpich3/man:$MANPATH

Exit the .bashrc file and execute the following command.Of course you can test your installation after execute the command with the help of mpirun -np k ./examples/cpi statement.

source .bashrc

FFTW

Second Let’s start the FFTW installation,you can download the source code from the official website and execute the following commands

tar -zxvf fftw
cd fftw-3.3.8
./configure --prefix=/home/day/material/lammps/fftw3/ --enable-shared=yes ( = you should remmember this path)
make -j n
make install

Okay It’s done!

5.2.1.2. Obtaining and building the Lammps¶

Next download the lammps source code and execute the following commands

tar -zxvf lammps
cd lammps-22Aug18/src
cd STUBS/
make
cd ../MAKE
vim Makefile.mpi(modify details see below)
cd ..
make mpi

When you finish the commands,you can see a executable file lmp_mpi in the src/ folder,you can make a directory lammps sibling directory and copy the lmp_mpi in this folder.Remmember to add the its path to .bashrc in order to you can call lammps command in any folders.

Note

If you want install the optional packages that extend LAMMPS functionality which enable a specific set of features.You can use the following command to check relative packages:

cd lammps-22Aug18/src
make package-status

And use the following commands to install and uninstall the packages.

make yes-package
make no-package

5.3. DL_POLY Tutorials¶

DL_POLY is a package of subroutines,programs and data files,designed to facilitate molecular dynamics simulations of macromolecules, polymers,ionic systems and solutions on a distributed memory parallel computer.

5.3.1. Install DL_POLY¶

In this section,I will show you the simplest way to install the DL_POLY in you Linux(Ubuntu) system.What you should install gfortran and MPICH in your computer before install the DL_POLY which are introduced in the Lammps Install section. Consequently you only need to download the source code from the official website and execute the following commands

unzip dl_poly_4.09.zip
cd dl_poly_4.09
cd source
ln -s ../build/Makefile-MPI Makefile
vim Makefile (**modify the Makefile**)
make hpc

If you want a JAVA-GUI to visualize your simulation system and examine basic properties,you should execute

cd ../java
./build

Okay you have install the DL_POLY in your PC and you can see a executable file DLPOLY.Z in the execute folder.Hope you have installed successfully!