def _overlap_AB_f90(atomlist1, atomlist2, valorbs1, valorbs2, SKT):
"""
This function calls an external Fortran function that computes the matrix elements.
Since hashes and tuples cannot be used easily in Fortran, the arguments are brought
into a form that can be fed into the Fortran function.
"""
atom_type_dic, spline_deg, tab_filled_SH0, tab_filled_D, \
(S_knots, S_coefs, H_knots, H_coefs, D_knots, D_coefs) = \
combine_slako_tables_f90(SKT)
# number of atoms
Nat1 = len(atomlist1)
Nat2 = len(atomlist2)
# orbitals
atom_indeces1, atom_types1, ls1, ms1 = atomlist2orbitals(
atomlist1, valorbs1, atom_type_dic)
atom_indeces2, atom_types2, ls2, ms2 = atomlist2orbitals(
atomlist2, valorbs2, atom_type_dic)
assert atom_indeces1 == atom_indeces2, "atomlist1 and atomlist2 should contain the same atoms in the same order!"
# count valence orbitals
Norb1 = len(ls1)
Norb2 = len(ls2)
# distances and direction
pos1 = XYZ.atomlist2vector(atomlist1)
pos1 = np.reshape(
pos1, (Nat1, 3)).transpose() # pos(:,i) is the 3d position of atom i
pos2 = XYZ.atomlist2vector(atomlist2)
pos2 = np.reshape(pos2, (Nat2, 3)).transpose()
r, x, y, z = slako.slako.directional_cosines(pos1, pos2)
# call Fortran function
S = slako.slako.overlap12(atom_indeces1, atom_types1, ls1, ms1,
atom_indeces2, atom_types2, ls2, ms2, r, x, y, z,
spline_deg, tab_filled_SH0, S_knots, S_coefs)
return S
def _DipoleMatrix_f90(atomlist1, atomlist2, valorbs, SKT, Mproximity, S):
"""
This function calls an external Fortran function that computes the matrix elements.
Since hashes and tuples cannot be used easily in Fortran, the arguments are brought
into a form that can be fed into the Fortran function.
"""
atom_type_dic, spline_deg, tab_filled_SH0, tab_filled_D, \
(S_knots, S_coefs, H_knots, H_coefs, D_knots, D_coefs) = \
combine_slako_tables_f90(SKT)
# number of atoms
Nat1 = len(atomlist1)
Nat2 = len(atomlist2)
# orbitals
atom_indeces1,atom_types1,ls1,ms1 = atomlist2orbitals(atomlist1, valorbs, atom_type_dic)
atom_indeces2,atom_types2,ls2,ms2 = atomlist2orbitals(atomlist2, valorbs, atom_type_dic)
assert atom_indeces1 == atom_indeces2, "atomlist1 and atomlist2 should contain the same atoms in the same order!"
# count valence orbitals
Norb1 = len(ls1)
Norb2 = len(ls2)
# distances and direction
pos1 = XYZ.atomlist2vector(atomlist1)
pos1 = np.reshape(pos1,(Nat1,3)).transpose() # pos(:,i) is the 3d position of atom i
pos2 = XYZ.atomlist2vector(atomlist2)
pos2 = np.reshape(pos2,(Nat2,3)).transpose()
r,x,y,z = slako.slako.directional_cosines(pos1,pos2)
Dipole = slako.slako.dipolematrix(atom_indeces1,atom_types1,ls1,ms1,
atom_indeces2,atom_types2,ls2,ms2,
r,x,y,z,pos1,
Mproximity,
S,
spline_deg, tab_filled_D,
D_knots, D_coefs)
# In fortran the faster indeces come first, roll axes D(xyz,mu,nu) -> D(mu,nu,xyz)
Dipole = np.rollaxis(Dipole,0,3)
return Dipole