Disable contribution from specific atoms

[tgmaxson]

According to this paper ( https://pubs.acs.org/doi/10.1021/acs.jpclett.3c00856 ) it seems that it may be reasonable to disable the D3 contributions arising from cations in some cases. This is implemented in CP2K by removing the energy, force, and stress terms involving the cation (but keeping the ion in the CN calculation I think) but not generally implemented anywhere else that I can find. Is this something that can be enabled for the ASE calculator of dftd3?

[awvwgk]

One option for implementing this would be to give a zero C6 coefficient to atoms marked as "ghost atom" in this case they would be fully accounted for in the CN calculation, but don't contribute to the energy, forces and stress directly.

[tgmaxson]

Is there a straightforward way to do this using the ASE calculator?

In VASP it looks like we can set the C6 per species, but I see no similar keyword for the ASE calculator.

[awvwgk]

The way for approaching this would add an option for the dispersion model to set C6 coefficients to zero, maybe here

simple-dftd3/src/dftd3/model.f90

Lines 128 to 140 in d9b9c7b

	allocate(self%c6(mref, mref, mol%nid, mol%nid), source=0.0_wp)
	do isp = 1, mol%nid
	izp = mol%num(isp)
	do jsp = 1, isp
	jzp = mol%num(jsp)
	do iref = 1, self%ref(isp)
	do jref = 1, self%ref(jsp)
	self%c6(jref, iref, jsp, isp) = get_c6(jref, iref, jzp, izp)
	self%c6(iref, jref, isp, jsp) = self%c6(jref, iref, jsp, isp)
	end do
	end do
	end do
	end do

The option could be added a logical / bool array which is initialized from a list of indices or by directly using a list of indices.

For usage in the ASE calculator we need to define the export in the C API first, maybe in a similar way like we set the real space cutoff in the model:

simple-dftd3/src/dftd3/api.f90

Lines 309 to 310 in d9b9c7b

	subroutine set_model_realspace_cutoff(verror, vdisp, disp2, disp3, cn) &
	& bind(C, name=namespace//"set_model_realspace_cutoff")

simple-dftd3/include/s-dftd3.h

Lines 119 to 125 in d9b9c7b

	/// Set realspace cutoffs (quantities in Bohr)
	SDFTD3_API_ENTRY void SDFTD3_API_CALL
	dftd3_set_model_realspace_cutoff(dftd3_error /* error */,
	dftd3_model /* model */,
	double /* disp2 */,
	double /* disp3 */,
	double /* cn */) SDFTD3_API_SUFFIX__V_0_5;

This gets forwarded to Python via the dftd3.library implementation, probably with a simple decoration of the C function as in

simple-dftd3/python/dftd3/library.py

Line 108 in d9b9c7b

set_model_realspace_cutoff = error_check(lib.dftd3_set_model_realspace_cutoff)

And than added as method for the DispersionModel defined in dftd3.interface

simple-dftd3/python/dftd3/interface.py

Lines 410 to 413 in d9b9c7b

	def set_realspace_cutoff(self, disp2: float, disp3: float, cn: float):
	"""Set realspace cutoff for evaluation of interactions"""
	library.set_model_realspace_cutoff(self._disp, disp2, disp3, cn)

With this we can include it in the ASE calculator for the default_parameters and set method implementation

simple-dftd3/python/dftd3/ase.py

Lines 143 to 148 in d9b9c7b

	default_parameters = {
	"method": None,
	"damping": None,
	"params_tweaks": {},
	"cache_api": True,
	}

simple-dftd3/python/dftd3/ase.py

Lines 180 to 189 in d9b9c7b

	def set(self, **kwargs) -> dict:
	"""Set new parameters to dftd3"""
	changed_parameters = Calculator.set(self, **kwargs)
	# Always reset the calculation if parameters change
	if changed_parameters:
	self.reset()
	return changed_parameters

It does involve all parts of the dftd3 library, so probably a good issue for somebody who would like to get started (when I have time in the coming weeks I might pick it up myself, but no promises on the estimated time of arrival).