Interfragments bonds

[RMeli]

Contrasting definitions of interfragment bonds.

Peng et al.:

If the molecular system consists of two or more fragments [...], then the shortest distance [d_min] between the fragments is determined; all interfragment distances [d] that are less than the smaller of 1.3 times this distance, or 2 angstrom, are designated as bonds.

This corresponds to the following condition:

d < min(1.3 * d_min, 2 * angstrom_to_bohr)

Bakken and Helgaker:

If two (or more) [...] fragments are found, the shortest bond between two atoms belonging to separate fragments [d_min] defines an interfragment bond coordinate. Other interfragment distances [d] that are either less than 2 angstrom or less than 1.3 times the interfragment bond coordinate constitute the auxiliary interfragment bonds.

This corresponds to the following condition:

d < max(1.3 * d_min, 2 * angstrom_to_bohr)

[RMeli]

Bonds between fragments made recursively between closest fragments until there are no fragments.

[RMeli]

Iterative search implemented and tested on H2O2 and H2+H2.

The function is quite complex and can still contain bugs. A refactoring is probably needed on a later stage.