occ::solvent::surface Namespace Reference

Classes
struct	Surface

Functions
Surface	solvent_surface (const Vec &radii, const IVec &atomic_numbers, const Mat3N &positions, double solvent_radius_angs=0.4, bool axis_aligned=true, double smoothing_width_bohr=0.0)
	Build an atom-centered Lebedev cavity surface.
IVec	nearest_atom_index (const Mat3N &atom_positions, const Mat3N &element_centers)

Function Documentation

nearest_atom_index()

IVec occ::solvent::surface::nearest_atom_index	(	const Mat3N &	atom_positions,
		const Mat3N &	element_centers
	)

solvent_surface()

Surface occ::solvent::surface::solvent_surface	(	const Vec &	radii,
		const IVec &	atomic_numbers,
		const Mat3N &	positions,
		double	solvent_radius_angs = 0.4,
		bool	axis_aligned = true,
		double	smoothing_width_bohr = 0.0
	)

Build an atom-centered Lebedev cavity surface.

axis_aligned = true (default) preserves the legacy behaviour of pre-rotating the molecule into its principal-axes frame before placing the Lebedev grid — fine for energy-only callers (SMD HF/DFT pipeline). For analytical gradients, set axis_aligned = false so each cavity point sits rigidly on its parent atom; otherwise the global rotation chain ∂axes/∂R breaks the frozen-cavity assumption in cosmo::gradient.

smoothing_width_bohr = 0 (default) uses the legacy boolean mask (point is either fully included or fully dropped). With smoothing_width_bohr > 0, each cavity point gets a continuous weight in [0, 1]:

weight_j = Π_{k ≠ atom_j} smoothstep(|r_j − R_k|, r_k, w)
smoothstep(d, t, w) = ½ (1 + erf((d − t)/w))

Distances are measured between the post-shift cavity vertex and atom centres so the gradient code can reconstruct the same weights from surface.vertices and atom radii. Areas are multiplied by the weight and points whose weight falls below 1e-10 are dropped. This makes the cavity, and any energy derived from it, C∞ with respect to atomic positions — required for clean analytical gradients.