def check_methyl_os_tpss(scf_solver):
"""Try to converge the SCF for the methyl radical molecule with the TPSS functional.
Parameters
----------
scf_solver : one of the SCFSolver types in HORTON
A configured SCF solver that must be tested.
"""
fn_fchk = context.get_fn('test/methyl_tpss_321g.fchk')
mol = IOData.from_file(fn_fchk)
grid = BeckeMolGrid(mol.coordinates, mol.numbers, mol.pseudo_numbers, 'fine',
random_rotate=False)
olp = mol.obasis.compute_overlap()
kin = mol.obasis.compute_kinetic()
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers)
er = mol.obasis.compute_electron_repulsion()
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UGridGroup(mol.obasis, grid, [
ULibXCMGGA('x_tpss'),
ULibXCMGGA('c_tpss'),
]),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
# compute the energy before converging
dm_alpha = mol.orb_alpha.to_dm()
dm_beta = mol.orb_beta.to_dm()
ham.reset(dm_alpha, dm_beta)
ham.compute_energy()
assert abs(ham.cache['energy'] - -39.6216986265) < 1e-3
# The convergence should be reasonable, not perfect because of limited
# precision in the molden file:
assert convergence_error_eigen(ham, olp, mol.orb_alpha, mol.orb_beta) < 1e-3
# keep a copy of the orbital energies
expected_alpha_energies = mol.orb_alpha.energies.copy()
expected_beta_energies = mol.orb_beta.energies.copy()
# Converge from scratch
occ_model = AufbauOccModel(5, 4)
check_solve(ham, scf_solver, occ_model, olp, kin, na, mol.orb_alpha, mol.orb_beta)
# test orbital energies
assert abs(mol.orb_alpha.energies - expected_alpha_energies).max() < 2e-3
assert abs(mol.orb_beta.energies - expected_beta_energies).max() < 2e-3
ham.compute_energy()
# compare with
assert abs(ham.cache['energy_kin'] - 38.98408965928) < 1e-2
assert abs(ham.cache['energy_ne'] - -109.2368837076) < 1e-2
assert abs(ham.cache['energy_hartree'] + ham.cache['energy_libxc_mgga_x_tpss'] +
ham.cache['energy_libxc_mgga_c_tpss'] - 21.55131145126) < 1e-2
assert abs(ham.cache['energy'] - -39.6216986265) < 1e-3
assert abs(ham.cache['energy_nn'] - 9.0797839705) < 1e-5
def check_lih_os_hf(scf_solver):
fn_fchk = context.get_fn('test/li_h_3-21G_hf_g09.fchk')
mol = IOData.from_file(fn_fchk)
olp = mol.obasis.compute_overlap(mol.lf)
kin = mol.obasis.compute_kinetic(mol.lf)
na = mol.obasis.compute_nuclear_attraction(mol.coordinates,
mol.pseudo_numbers, mol.lf)
er = mol.obasis.compute_electron_repulsion(mol.lf)
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UExchangeTerm(er, 'x_hf'),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
occ_model = AufbauOccModel(2, 1)
check_solve(ham, scf_solver, occ_model, mol.lf, olp, kin, na,
mol.exp_alpha, mol.exp_beta)
expected_alpha_energies = np.array([
-2.76116635E+00,
-7.24564188E-01,
-1.79148636E-01,
-1.28235698E-01,
-1.28235698E-01,
-7.59817520E-02,
-1.13855167E-02,
6.52484445E-03,
6.52484445E-03,
7.52201895E-03,
9.70893294E-01,
])
expected_beta_energies = np.array([
-2.76031162E+00,
-2.08814026E-01,
-1.53071066E-01,
-1.25264964E-01,
-1.25264964E-01,
-1.24605870E-02,
5.12761388E-03,
7.70499854E-03,
7.70499854E-03,
2.85176080E-02,
1.13197479E+00,
])
assert abs(mol.exp_alpha.energies - expected_alpha_energies).max() < 1e-5
assert abs(mol.exp_beta.energies - expected_beta_energies).max() < 1e-5
ham.compute_energy()
# compare with g09
assert abs(ham.cache['energy'] - -7.687331212191962E+00) < 1e-8
assert abs(ham.cache['energy_kin'] - 7.640603924034E+00) < 2e-7
assert abs(ham.cache['energy_hartree'] + ham.cache['energy_x_hf'] -
2.114420907894E+00) < 1e-7
assert abs(ham.cache['energy_ne'] - -1.811548789281E+01) < 2e-7
assert abs(ham.cache['energy_nn'] - 0.6731318487) < 1e-8
def check_h3_os_pbe(scf_solver):
fn_fchk = context.get_fn("test/h3_pbe_321g.fchk")
mol = IOData.from_file(fn_fchk)
grid = BeckeMolGrid(mol.coordinates, mol.numbers, mol.pseudo_numbers, "veryfine", random_rotate=False)
olp = mol.obasis.compute_overlap(mol.lf)
kin = mol.obasis.compute_kinetic(mol.lf)
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers, mol.lf)
er = mol.obasis.compute_electron_repulsion(mol.lf)
external = {"nn": compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [
UTwoIndexTerm(kin, "kin"),
UDirectTerm(er, "hartree"),
UGridGroup(mol.obasis, grid, [ULibXCGGA("x_pbe"), ULibXCGGA("c_pbe")]),
UTwoIndexTerm(na, "ne"),
]
ham = UEffHam(terms, external)
# compute the energy before converging
dm_alpha = mol.exp_alpha.to_dm()
dm_beta = mol.exp_beta.to_dm()
ham.reset(dm_alpha, dm_beta)
ham.compute_energy()
assert abs(ham.cache["energy"] - -1.593208400939354e00) < 1e-5
# The convergence should be reasonable, not perfect because of limited
# precision in Gaussian fchk file:
assert convergence_error_eigen(ham, mol.lf, olp, mol.exp_alpha, mol.exp_beta) < 2e-6
# Converge from scratch
occ_model = AufbauOccModel(2, 1)
check_solve(ham, scf_solver, occ_model, mol.lf, olp, kin, na, mol.exp_alpha, mol.exp_beta)
# test orbital energies
expected_energies = np.array(
[-5.41141676e-01, -1.56826691e-01, 2.13089637e-01, 7.13565167e-01, 7.86810564e-01, 1.40663544e00]
)
assert abs(mol.exp_alpha.energies - expected_energies).max() < 2e-5
expected_energies = np.array(
[-4.96730336e-01, -5.81411249e-02, 2.73586652e-01, 7.41987185e-01, 8.76161160e-01, 1.47488421e00]
)
assert abs(mol.exp_beta.energies - expected_energies).max() < 2e-5
ham.compute_energy()
# compare with g09
assert abs(ham.cache["energy_ne"] - -6.934705182067e00) < 1e-5
assert abs(ham.cache["energy_kin"] - 1.948808793424e00) < 1e-5
assert (
abs(
ham.cache["energy_hartree"]
+ ham.cache["energy_libxc_gga_x_pbe"]
+ ham.cache["energy_libxc_gga_c_pbe"]
- 1.502769385597e00
)
< 1e-5
)
assert abs(ham.cache["energy"] - -1.593208400939354e00) < 1e-5
assert abs(ham.cache["energy_nn"] - 1.8899186021) < 1e-8
def check_lih_os_hf(scf_solver):
fn_fchk = context.get_fn("test/li_h_3-21G_hf_g09.fchk")
mol = IOData.from_file(fn_fchk)
olp = mol.obasis.compute_overlap(mol.lf)
kin = mol.obasis.compute_kinetic(mol.lf)
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers, mol.lf)
er = mol.obasis.compute_electron_repulsion(mol.lf)
external = {"nn": compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [UTwoIndexTerm(kin, "kin"), UDirectTerm(er, "hartree"), UExchangeTerm(er, "x_hf"), UTwoIndexTerm(na, "ne")]
ham = UEffHam(terms, external)
occ_model = AufbauOccModel(2, 1)
check_solve(ham, scf_solver, occ_model, mol.lf, olp, kin, na, mol.exp_alpha, mol.exp_beta)
expected_alpha_energies = np.array(
[
-2.76116635e00,
-7.24564188e-01,
-1.79148636e-01,
-1.28235698e-01,
-1.28235698e-01,
-7.59817520e-02,
-1.13855167e-02,
6.52484445e-03,
6.52484445e-03,
7.52201895e-03,
9.70893294e-01,
]
)
expected_beta_energies = np.array(
[
-2.76031162e00,
-2.08814026e-01,
-1.53071066e-01,
-1.25264964e-01,
-1.25264964e-01,
-1.24605870e-02,
5.12761388e-03,
7.70499854e-03,
7.70499854e-03,
2.85176080e-02,
1.13197479e00,
]
)
assert abs(mol.exp_alpha.energies - expected_alpha_energies).max() < 1e-5
assert abs(mol.exp_beta.energies - expected_beta_energies).max() < 1e-5
ham.compute_energy()
# compare with g09
assert abs(ham.cache["energy"] - -7.687331212191962e00) < 1e-8
assert abs(ham.cache["energy_kin"] - 7.640603924034e00) < 2e-7
assert abs(ham.cache["energy_hartree"] + ham.cache["energy_x_hf"] - 2.114420907894e00) < 1e-7
assert abs(ham.cache["energy_ne"] - -1.811548789281e01) < 2e-7
assert abs(ham.cache["energy_nn"] - 0.6731318487) < 1e-8
def check_h3_os_pbe(scf_solver):
fn_fchk = context.get_fn('test/h3_pbe_321g.fchk')
mol = IOData.from_file(fn_fchk)
grid = BeckeMolGrid(mol.coordinates, mol.numbers, mol.pseudo_numbers, 'veryfine', random_rotate=False)
olp = mol.obasis.compute_overlap()
kin = mol.obasis.compute_kinetic()
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers)
er = mol.obasis.compute_electron_repulsion()
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UGridGroup(mol.obasis, grid, [
ULibXCGGA('x_pbe'),
ULibXCGGA('c_pbe'),
]),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
# compute the energy before converging
dm_alpha = mol.orb_alpha.to_dm()
dm_beta = mol.orb_beta.to_dm()
ham.reset(dm_alpha, dm_beta)
ham.compute_energy()
assert abs(ham.cache['energy'] - -1.593208400939354E+00) < 1e-5
# The convergence should be reasonable, not perfect because of limited
# precision in Gaussian fchk file:
assert convergence_error_eigen(ham, olp, mol.orb_alpha, mol.orb_beta) < 2e-6
# Converge from scratch
occ_model = AufbauOccModel(2, 1)
check_solve(ham, scf_solver, occ_model, olp, kin, na, mol.orb_alpha, mol.orb_beta)
# test orbital energies
expected_energies = np.array([
-5.41141676E-01, -1.56826691E-01, 2.13089637E-01, 7.13565167E-01,
7.86810564E-01, 1.40663544E+00
])
assert abs(mol.orb_alpha.energies - expected_energies).max() < 2e-5
expected_energies = np.array([
-4.96730336E-01, -5.81411249E-02, 2.73586652E-01, 7.41987185E-01,
8.76161160E-01, 1.47488421E+00
])
assert abs(mol.orb_beta.energies - expected_energies).max() < 2e-5
ham.compute_energy()
# compare with g09
assert abs(ham.cache['energy_ne'] - -6.934705182067E+00) < 1e-5
assert abs(ham.cache['energy_kin'] - 1.948808793424E+00) < 1e-5
assert abs(ham.cache['energy_hartree'] + ham.cache['energy_libxc_gga_x_pbe'] + ham.cache['energy_libxc_gga_c_pbe'] - 1.502769385597E+00) < 1e-5
assert abs(ham.cache['energy'] - -1.593208400939354E+00) < 1e-5
assert abs(ham.cache['energy_nn'] - 1.8899186021) < 1e-8
def compute_hf_energy(mol):
olp = mol.obasis.compute_overlap(mol.lf)
kin = mol.obasis.compute_kinetic(mol.lf)
na = mol.obasis.compute_nuclear_attraction(mol.coordinates,
mol.pseudo_numbers, mol.lf)
er = mol.obasis.compute_electron_repulsion(mol.lf)
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
if hasattr(mol, 'exp_beta'):
# assuming unrestricted
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UExchangeTerm(er, 'x_hf'),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
dm_alpha = mol.exp_alpha.to_dm()
dm_beta = mol.exp_beta.to_dm()
ham.reset(dm_alpha, dm_beta)
else:
# assuming restricted
terms = [
RTwoIndexTerm(kin, 'kin'),
RDirectTerm(er, 'hartree'),
RExchangeTerm(er, 'x_hf'),
RTwoIndexTerm(na, 'ne'),
]
ham = REffHam(terms, external)
dm_alpha = mol.exp_alpha.to_dm()
ham.reset(dm_alpha)
return ham.compute_energy()
def compute_hf_energy(mol):
olp = mol.obasis.compute_overlap(mol.lf)
kin = mol.obasis.compute_kinetic(mol.lf)
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers, mol.lf)
er = mol.obasis.compute_electron_repulsion(mol.lf)
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
if hasattr(mol, 'exp_beta'):
# assuming unrestricted
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UExchangeTerm(er, 'x_hf'),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
dm_alpha = mol.exp_alpha.to_dm()
dm_beta = mol.exp_beta.to_dm()
ham.reset(dm_alpha, dm_beta)
else:
# assuming restricted
terms = [
RTwoIndexTerm(kin, 'kin'),
RDirectTerm(er, 'hartree'),
RExchangeTerm(er, 'x_hf'),
RTwoIndexTerm(na, 'ne'),
]
ham = REffHam(terms, external)
dm_alpha = mol.exp_alpha.to_dm()
ham.reset(dm_alpha)
return ham.compute_energy()
def check_lih_os_hf(scf_solver):
fn_fchk = context.get_fn('test/li_h_3-21G_hf_g09.fchk')
mol = IOData.from_file(fn_fchk)
olp = mol.obasis.compute_overlap()
kin = mol.obasis.compute_kinetic()
na = mol.obasis.compute_nuclear_attraction(mol.coordinates, mol.pseudo_numbers)
er = mol.obasis.compute_electron_repulsion()
external = {'nn': compute_nucnuc(mol.coordinates, mol.pseudo_numbers)}
terms = [
UTwoIndexTerm(kin, 'kin'),
UDirectTerm(er, 'hartree'),
UExchangeTerm(er, 'x_hf'),
UTwoIndexTerm(na, 'ne'),
]
ham = UEffHam(terms, external)
occ_model = AufbauOccModel(2, 1)
check_solve(ham, scf_solver, occ_model, olp, kin, na, mol.orb_alpha, mol.orb_beta)
expected_alpha_energies = np.array([
-2.76116635E+00, -7.24564188E-01, -1.79148636E-01, -1.28235698E-01,
-1.28235698E-01, -7.59817520E-02, -1.13855167E-02, 6.52484445E-03,
6.52484445E-03, 7.52201895E-03, 9.70893294E-01,
])
expected_beta_energies = np.array([
-2.76031162E+00, -2.08814026E-01, -1.53071066E-01, -1.25264964E-01,
-1.25264964E-01, -1.24605870E-02, 5.12761388E-03, 7.70499854E-03,
7.70499854E-03, 2.85176080E-02, 1.13197479E+00,
])
assert abs(mol.orb_alpha.energies - expected_alpha_energies).max() < 1e-5
assert abs(mol.orb_beta.energies - expected_beta_energies).max() < 1e-5
ham.compute_energy()
# compare with g09
assert abs(ham.cache['energy'] - -7.687331212191962E+00) < 1e-8
assert abs(ham.cache['energy_kin'] - 7.640603924034E+00) < 2e-7
assert abs(ham.cache['energy_hartree'] + ham.cache['energy_x_hf'] - 2.114420907894E+00) < 1e-7
assert abs(ham.cache['energy_ne'] - -1.811548789281E+01) < 2e-7
assert abs(ham.cache['energy_nn'] - 0.6731318487) < 1e-8