Ab-initio Molecular Dynamics (VASP)

Ab-initio Molecular Dynamics (AIMD) is a computational method that uses first principles to simulate the motion of atoms in a system. It is a type of molecular dynamics (MD) simulation that does not rely on empirical potentials or force fields to describe the interactions between atoms, but rather calculates these interactions directly from the electronic structure of the system using quantum mechanics.

In an ab initio MD simulation, the total energy of the system is calculated at each time step using density functional theory (DFT) or another method of quantum chemistry. The forces acting on each atom are then determined from the gradient of the energy with respect to the atomic coordinates, and the equations of motion are solved to predict the trajectory of the atoms.

This document aims to record and summarize the computational details of AIMD simulation using VASP.

1 Input

1.1 POSCAR

Preparing a  sufficiently large supercell (2$\times$2$\times$2, for example).

You can obtain it by following the description in: Preparing a Super Cell - VASP Wiki, or using VASPKIT via the following command line:

echo -e "401\n1\n2 2 2\n"|vaspkit
mv SC222.vasp POSCAR

Note:

If a continuation run is performed copy CONTCAR to POSCAR or possibly deliver initial velocities in the POSCAR file. They are written after the Wycoff positions in an own paragraph. If no initial velocities are provided random velocities are assumed at the beginning of the calculation. This is fully ok but the user should be aware that due to the initial random velocities the trajectories obtained from different calculations are difficult to compare.

1.2 INCAR

SYSTEM = Ab-initio MD

# ab initio
ISMEAR = 0        # Gaussian smearing
SIGMA  = 0.05     # smearing in eV

LREAL  = Auto     # projection operators in real space

ALGO   = Fast     # RMM-DIIS for electronic relaxation
PREC   = Normal   # precision
ISYM   = 0        # no symmetry imposed

# MD
IBRION = 0        # enable a molecular dynamics calculation
NSW    = 5000     # number of steps
POTIM  = 2.0      # MD time step in fs

MDALGO = 2        # Nosé-Hoover thermostat
ISIF   = 2
SMASS  = 1.0      # Nosé mass

TEBEG  = 1000     # temperature at beginning
TEEND  = 1000     # temperature at end

NCORE  = 2        # parallelization

Thermostats are used in molecular-dynamics calculations within the NVT ensemble and NpT ensemble in order to apply a certain temperature to the ionic degrees of freedom.

1.3 KPOINTS

K-Points
 0
Gamma
 1  1  1
 0  0  0

Since a sufficiently large super cell is used in MD, it is ok in this case to use only a single k-point in the calculations. Hence it is also possible to use the $\Gamma$-point only version which is significantly faster than the standard version.

1.4 POTCAR

Pseudopotentials of the system

2 Output

2.1 Pair correlation function

The pair correlation function is written out to the PCDAT file. The abscissa of that file is within mesh points of a selected grid and need to be converted to $\AA$. This is done by invoking the following short awk script on the command line:

awk <PCDAT >PCDAT.10ps ' NR==8 {pcskal=$1} NR==9 {pcfein=$1} NR>=13 {line=line+1; print (line-0.5)*pcfein/pcskal,$1} '

Also, you can do this via VASPKIT:

echo -e "725\n"|vaspkit

Solids usually show sharp peaks in the pair correlation function since the ions only vibrate around fixed positions in the crystal lattice. In the liquid or amorphous state the distances are much more diffuse and one usually would expect no far order (but both can have near order).

2.2 Energy conservation

We can output the total energy for each molecular dynamics step by invoking the command:

grep "free  energy" OUTCAR|awk ' {print $5}' >> energy.dat

Reference:

• Molecular dynamics calculations

• Molecular dynamics

• Molecular dynamics - Tutorial