esta.externalBag.get_connection
¶
connectivity_bond_list_(atm_position, atm_symbol, cutoff=None)
¶
similar to connectivity_bond_list, but now atm_position and atm_symbol are directly input instead of xyz file
connectivity_matrix_(atm_position, atm_symbol, cutoff=None)
¶
parameters:
atm_position: rank 2 array atomic positions atm_symbol: list list of atom symobols cutoff: dict dict containing atomic symobols and atomic radii as key-values; e.g cutoff={'H':0.4, 'P':1.0}. Radii are in angstrom
return:
c_matrix: rank 2 array matrix containing 1' and 0' for showing atomic connection between atoms in atomic systems