code: def _jit_give_bond_array(pos, bond_radii, self_bonding_allowed=False):
          
          n = pos.shape[0]
          bond_array = np.empty((n, n), dtype=nb.boolean)
  
          for i in range(n):
              for j in range(i, n):
                  D = 0
                  for h in range(3):
                      D += (pos[i, h] - pos[j, h])**2
                  B = (bond_radii[i] + bond_radii[j])**2
                  bond_array[i, j] = (B - D) >= 0
                  bond_array[j, i] = bond_array[i, j]
          if not self_bonding_allowed:
              for i in range(n):
                  bond_array[i, i] = False
          return bond_array
docs: Calculate a boolean array where ``A[i,j] is True`` indicates a
          bond between the i-th and j-th atom.