The DFT-D2 method by Grimme  is supported to include a vdW interaction. The following keywords are relevant to the DFT-D2 method.
scf.dftD on # on|off, default=off DFTD.Unit Ang # Ang|AU DFTD.rcut_dftD 100.0 # default=100 (DFTD.Unit) DFTD.d 20.0 # default=20 DFTD.scale6 0.75 # default=0.75 DFTD.IntDirection 1 1 1 # default=1 1 1 (1:on 0:off)When you include the vdW correction, switch 'scf.dftD' on. The cutoff radius for the pairwise interaction is given by 'DFTD.rcut_dftD', where the unit is given by 'DFTD.Unit'. The 'd' value in Eq.(12) in Grimme's paper  is given by 'DFTD.d', while the default value is 20. The scaling factor in Eq. (11) in Grimme's papar  is given by 'DFTD.scale6', while the default value for the PBE functional is 0.75. Also, the interaction can be cut along the a-, b-, and c-axes by 'DFTD.IntDirection', where 1 means that the interaction is included, and 0 not. Also, the periodicity for each atom can be controlled by
<DFTD.periodicity 1 1 2 1 3 1 4 1 .... DFTD.periodicity>where the first column is a serial number which is the same as in the 'Atoms.SpeciesAndCoordinates', and the second column is a flag which means that 1 is periodic, and 0 is non-periodic for the corresponding atom. By considering the periodicity or non-periodicity of each atom, the interaction is automatically cut when they are non-periodic.
The main modifications are placed at only two routines: DFTDvdW_init.c and Calc_EdftD() of Total_Energy.c. In DFTDvdW_init.c, you can easily change the parameters for the vdW correction, and in Calc_EdftD() of Total_Energy.c you can confirm how they are calculated.
Since OpenMX uses localized orbitals as basis function, it is very important to take account of basis set superposition error (BSSE) when we investigate an effect of a weak interaction such as vdW interaction. To estimate BSSE, the counterpoise (CP) method [29,30] can be used. As for the CP method see the section 'Empty atom scheme'.