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get_atom_orb.py
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import pyscf
import Driver_SCF
Atom_Info = {
'C': {
"charge_fake": 2,
"spin": 2,
"state": [[0, 'b1g', 1], [0, 'b2g', 1], [0, 'b3g', 1]],
"nelec": (2, 0)
},
'Si': {
"charge_fake": 2,
"spin": 2,
"state": [[0, 'b1g', 1], [0, 'b2g', 1], [0, 'b3g', 1]],
"nelec": (2, 0)
},
'N': {
"charge_fake": 3,
"spin": 3,
"state": [[1, 'au', 1]],
"nelec": (3, 0)
},
'P': {
"charge_fake": 3,
"spin": 3,
"state": [[1, 'au', 1]],
"nelec": (3, 0)
},
'O': {
"charge_fake": 4,
"spin": 2,
"state": [[0, 'b1g', 1], [0, 'b2g', 1], [0, 'b3g', 1]],
"nelec": (3, 1)
},
'S': {
"charge_fake": 4,
"spin": 2,
"state": [[0, 'b1g', 1], [0, 'b2g', 1], [0, 'b3g', 1]],
"nelec": (3, 1)
},
'F': {
"charge_fake": -1,
"spin": 1,
"state": [[1, 'b1u', 1], [1, 'b2u', 1], [1, 'b3u', 1]],
"nelec": (3, 2)
},
'Cl': {
"charge_fake": -1,
"spin": 1,
"state": [[1, 'b1u', 1], [1, 'b2u', 1], [1, 'b3u', 1]],
"nelec": (3, 2)
},
}
def _remove_orb_other_than_sp(energy, start_indx):
energy_now = 1e10
multi = 0
orb_indx = []
res = []
for indx in range(start_indx, len(energy)):
if abs(energy[indx]-energy_now) > 1e-8:
if multi >= 5:
res.extend(orb_indx)
energy_now = energy[indx]
multi = 1
orb_indx = [indx]
else:
orb_indx.append(indx)
multi += 1
if multi >= 5:
res.extend(orb_indx)
return res
def _label_atom_orb(energy):
orb_info = [["s", 0], ["p", 1], ["d", 2], ["f", 3], ["g", 4], ["h", 5]]
energy_now = 1e10
multi = 0
res = {}
orb_indx = []
for indx in range(0, len(energy)):
if abs(energy[indx]-energy_now) > 1e-8 and multi != 0:
l = (multi-1)//2
orb_info[l][1] += 1
res[str(orb_info[l][1])+orb_info[l][0]] = orb_indx
# print(res)
energy_now = energy[indx]
multi = 1
orb_indx = [indx]
else:
orb_indx.append(indx)
multi += 1
l = (multi-1)//2
orb_info[l][1] += 1
res[str(orb_info[l][1])+orb_info[l][0]] = orb_indx
return res
def _atom_min_cas(atom_label, basis='6-31G(d)', print_verbose=0):
if atom_label == "H":
mol = pyscf.gto.M(
verbose=print_verbose,
atom='''
H 0.000000000000 0.000000000000 0.000000000000
''',
basis=basis,
spin=1,
charge=0,
symmetry='d2h',
)
mol.build()
scf = pyscf.scf.ROHF(mol)
scf.kernel()
return [scf.mo_energy, scf.mo_coeff, _label_atom_orb(scf.mo_energy)]
else:
mol = pyscf.gto.M(
verbose=print_verbose,
atom='''
%s 0.000000000000 0.000000000000 0.000000000000
''' % (atom_label),
basis=basis,
spin=Atom_Info[atom_label]["spin"],
charge=0,
symmetry='d2h',
)
mol.build()
mol_fake = pyscf.gto.M(
verbose=print_verbose,
atom='''
%s 0.000000000000 0.000000000000 0.000000000000
''' % (atom_label),
basis=basis,
spin=0,
charge=Atom_Info[atom_label]["charge_fake"],
symmetry='d2h',
)
mol_fake.build()
scf_fake = Driver_SCF.Run_SCF(mol_fake)
scf = pyscf.scf.ROHF(mol)
scf.mo_coeff = scf_fake.mo_coeff
if print_verbose >= 10:
print(scf.mo_coeff[:, -2])
frozen = _remove_orb_other_than_sp(scf_fake.mo_energy, 5)
if (len(frozen) == 0):
frozen = None
min_cas = Driver_SCF.Run_MCSCF(mol, scf, Atom_Info[atom_label]["nelec"], 3,
_pyscf_state=Atom_Info[atom_label]["state"], _frozen=frozen)
if print_verbose >= 10:
print(min_cas.mo_coeff[:, -2])
scf.mo_coeff = min_cas.mo_coeff
min_cas_ = Driver_SCF.Run_MCSCF(mol, scf, Atom_Info[atom_label]["nelec"], 3, _mc_max_macro=0,
_pyscf_state=Atom_Info[atom_label]["state"])
if print_verbose >= 10:
print(min_cas_.mo_coeff[:, -2])
return [min_cas_.mo_energy, min_cas_.mo_coeff, _label_atom_orb(min_cas_.mo_energy)]
def atom_min_cas_bas(atom_label_list, basis='6-31G(d)', print_verbose=0):
res = {}
res['basis'] = basis
for atom in atom_label_list:
a, b, c = _atom_min_cas(atom, basis, print_verbose)
res[atom] = b
res[atom+"_bas_label"] = c
if print_verbose >= 10:
print(a)
print(c)
return res
if __name__ == "__main__":
print(_atom_min_cas("C")[1][:,2:5])
# print(_atom_min_cas("H")[1][:,2:5])
# print(_atom_min_cas("O")[1][:,2:5])
# print(_atom_min_cas("N")[1][:,2:5])
a, b = _atom_min_cas("C", basis='ccpvqz', print_verbose=0)
print(a, b[:, :5])
a, b = _atom_min_cas("H", basis='ccpvqz', print_verbose=0)
print(a, b[:, :5])
a, b = _atom_min_cas("O", basis='ccpvqz', print_verbose=0)
print(a, b[:, :5])
a, b = _atom_min_cas("N", basis='ccpvqz', print_verbose=0)
print(a, b[:, :5])