D3 Correction

The D3 extension is using Stefan Grimme’s DFT-D3 code. More information about the theory and supported functionals can be found here. The D3 correction helps to capture long range effects that are not present in most functionals. Because of this it becomes important in systems where for example the Van der Waals force plays a major role.

Usage

The D3 extension has one mandatory keyword, xc, which is what exchange-correlation functional to use.

An example of a system where the D3 correction adds a meaningful correction is in the case of 2D bilayer systems because of the Van der Waals interaction between the two layers.

from gpaw import GPAW
from gpaw.extensions.d3 import D3
from gpaw import PW
from ase.build import mx2

MoS2 = mx2('MoS2', a=3.2)
WSe2 = mx2('WSe2', a=3.2)

# 6.6Å of distance between layers
MoS2.positions[:, 2] += 3.3
WSe2.positions[:, 2] -= 3.3

bilayer = WSe2 + MoS2
bilayer.center(vacuum=6.0, axis=2)
bilayer.pbc = True  # suppress the D3 warning

calc = GPAW(mode=PW(400),
            xc='PBE',
            extensions=[D3(xc='PBE')],
            txt='out.txt')

bilayer.calc = calc
energy = bilayer.get_potential_energy()

# Acces the D3 correction energy
d3_correction = bilayer.calc.dft.d3.get_energy()

Note

D3 requires the system to either not be periodic or periodic in all three directions. If the system is only periodic in one or two directions a warning will appear and it will assume that the system is periodic in all three directions.

Output

The D3 correction is accessed by calling the get_energy() method on the d3 object as in the last line above. The result can also be found in the output file just after the list of iterations. For the above example the relevant part of the out.txt file will look as following:

...
Energy contributions relative to reference atoms: (reference = -702828.048343)

kinetic:          71.457107
coulomb:         -50.449930
zero:             -0.629602
external:          0.000000
xc:              -44.310857
entropy:          -0.001037
spinorbit:         0.000000
--------extensions:---------
D3 (xc=PBE):      -1.446148
----------------------------
Free energy:     -25.380467
Extrapolated:    -25.379948
...