def test_ao2mo_hand_against_pyscf_rhf_partial():
mol = molecules_pyscf.molecule_physicists_water_sto3g()
mol.build()
mf = pyscf.scf.RHF(mol)
mf.kernel()
C = fix_mocoeffs_shape(mf.mo_coeff)
occupations = occupations_from_pyscf_mol(mol, C)
nocc, nvirt, _, _ = occupations
nmo = nocc + nvirt
ntransforms = 2
o = slice(0, nocc)
v = slice(nocc, nmo)
ao2mo = AO2MOpyscf(C, verbose=mol.verbose, pyscfmol=mol)
ao2mo.perform_rhf_partial()
assert len(ao2mo.tei_mo) == ntransforms
tei_mo_ovov_pyscf = ao2mo.tei_mo[0]
tei_mo_oovv_pyscf = ao2mo.tei_mo[1]
tei_ao = mol.intor("int2e_sph", aosym="s1")
print("1. Use the class method explicitly.")
tei_mo_ovov_hand = AO2MO.transform(
tei_ao, C[0, :, o], C[0, :, v], C[0, :, o], C[0, :, v]
)
tei_mo_oovv_hand = AO2MO.transform(
tei_ao, C[0, :, o], C[0, :, o], C[0, :, v], C[0, :, v]
)
assert tei_mo_ovov_pyscf.shape == tei_mo_ovov_hand.shape == (nocc, nvirt, nocc, nvirt)
assert tei_mo_oovv_pyscf.shape == tei_mo_oovv_hand.shape == (nocc, nocc, nvirt, nvirt)
np.testing.assert_allclose(tei_mo_ovov_hand, tei_mo_ovov_pyscf, rtol=0, atol=1.0e-15)
np.testing.assert_allclose(tei_mo_oovv_hand, tei_mo_oovv_pyscf, rtol=0, atol=1.0e-15)
print("2. Use the class method normally.")
ao2mo_method = AO2MO(C, occupations, verbose=mol.verbose, I=tei_ao)
ao2mo_method.perform_rhf_partial()
assert len(ao2mo_method.tei_mo) == ntransforms
tei_mo_ovov_method = ao2mo_method.tei_mo[0]
tei_mo_oovv_method = ao2mo_method.tei_mo[1]
assert (
tei_mo_ovov_pyscf.shape == tei_mo_ovov_method.shape == (nocc, nvirt, nocc, nvirt)
)
assert (
tei_mo_oovv_pyscf.shape == tei_mo_oovv_method.shape == (nocc, nocc, nvirt, nvirt)
)
np.testing.assert_allclose(
tei_mo_ovov_method, tei_mo_ovov_pyscf, rtol=0, atol=1.0e-15
)
np.testing.assert_allclose(
tei_mo_oovv_method, tei_mo_oovv_pyscf, rtol=0, atol=1.0e-15
)
return
def test_explicit_rhf_outside_solver_off_diagonal_blocks():
mol = molecules.molecule_water_sto3g()
mol.build()
mf = pyscf.scf.RHF(mol)
mf.kernel()
mocoeffs = mf.mo_coeff
moenergies = mf.mo_energy
ao2mo = AO2MOpyscf(mocoeffs, mol.verbose, mol)
ao2mo.perform_rhf_full()
tei_mo = ao2mo.tei_mo[0]
C = mocoeffs
E = np.diag(moenergies)
occupations = utils.occupations_from_pyscf_mol(mol, mocoeffs)
nocc, nvirt, _, _ = occupations
A = eqns.form_rpa_a_matrix_mo_singlet_full(E, tei_mo, nocc)
B = eqns.form_rpa_b_matrix_mo_singlet_full(tei_mo, nocc)
G = np.block([[A, B], [B, A]])
assert G.shape == (2 * nocc * nvirt, 2 * nocc * nvirt)
G_inv = np.linalg.inv(G)
components = 3
integrals_dipole_ao = mol.intor("cint1e_r_sph", comp=components)
integrals_dipole_mo_ai = []
for component in range(components):
integrals_dipole_mo_ai_component = np.dot(
C[:, nocc:].T,
np.dot(integrals_dipole_ao[component, ...],
C[:, :nocc])).reshape(-1, order="F")
integrals_dipole_mo_ai.append(integrals_dipole_mo_ai_component)
integrals_dipole_mo_ai = np.stack(integrals_dipole_mo_ai, axis=0).T
integrals_dipole_mo_ai_super = np.concatenate(
(integrals_dipole_mo_ai, -integrals_dipole_mo_ai), axis=0)
rhsvecs = integrals_dipole_mo_ai_super
rspvecs = np.dot(G_inv, rhsvecs)
polarizability = 4 * np.dot(rhsvecs.T, rspvecs) / 2
# pylint: disable=bad-whitespace
result__0_00 = np.array([[7.93556221, 0.0, 0.0], [0.0, 3.06821077, 0.0],
[0.0, 0.0, 0.05038621]])
atol = 1.0e-8
rtol = 0.0
np.testing.assert_allclose(polarizability,
result__0_00,
rtol=rtol,
atol=atol)
def test_uncoupled_rhf() -> None:
mol = molecules.molecule_trithiolane_sto3g()
mol.build()
mf = pyscf.scf.RHF(mol)
mf.scf()
C = utils.fix_mocoeffs_shape(mf.mo_coeff)
E = utils.fix_moenergies_shape(mf.mo_energy)
occupations = occupations_from_pyscf_mol(mol, C)
solver = solvers.ExactInv(C, E, occupations)
ao2mo = AO2MOpyscf(C, mol.verbose, mol)
ao2mo.perform_rhf_partial()
solver.tei_mo = ao2mo.tei_mo
solver.tei_mo_type = AO2MOTransformationType.partial
driver = cphf.CPHF(solver)
operator_diplen = operators.Operator(label="dipole",
is_imaginary=False,
is_spin_dependent=False,
triplet=False)
integrals_diplen_ao = mol.intor("cint1e_r_sph", comp=3)
operator_diplen.ao_integrals = integrals_diplen_ao
driver.add_operator(operator_diplen)
frequencies = [0.0, 0.0773178, 0.128347]
driver.set_frequencies(frequencies)
driver.run(
hamiltonian=Hamiltonian.RPA,
spin=Spin.singlet,
program=Program.PySCF,
program_obj=mol,
)
for idxf, frequency in enumerate(frequencies):
print(idxf, frequency)
print("uncoupled")
diag_res = np.diag(driver.uncoupled_results[idxf])
diag_ref = np.diag(rhf_uncoupled[frequency]["result"])
diff = diag_res - diag_ref
print(diag_res)
print(diag_ref)
print(diff)
assert np.max(
np.abs(diff)) < rhf_uncoupled[frequency]["error_max_diag"]
print("coupled")
diag_res = np.diag(driver.results[idxf])
diag_ref = np.diag(rhf_coupled[frequency]["result"])
diff = diag_res - diag_ref
print(diag_res)
print(diag_ref)
print(diff)
assert np.max(np.abs(diff)) < rhf_coupled[frequency]["error_max_diag"]
def test_uncoupled_uhf():
mol = molecules.molecule_trithiolane_sto3g()
mol.charge = 1
mol.spin = 1
mol.build()
mf = pyscf.scf.uhf.UHF(mol)
mf.scf()
C = utils.fix_mocoeffs_shape(mf.mo_coeff)
E = utils.fix_moenergies_shape(mf.mo_energy)
occupations = utils.occupations_from_pyscf_mol(mol, C)
solver = iterators.ExactInv(C, E, occupations)
ao2mo = AO2MOpyscf(C, mol.verbose, mol)
ao2mo.perform_uhf_partial()
solver.tei_mo = ao2mo.tei_mo
solver.tei_mo_type = "partial"
driver = cphf.CPHF(solver)
operator_diplen = operators.Operator(
label="dipole", is_imaginary=False, is_spin_dependent=False, triplet=False
)
integrals_diplen_ao = mol.intor("cint1e_r_sph", comp=3)
operator_diplen.ao_integrals = integrals_diplen_ao
driver.add_operator(operator_diplen)
frequencies = [0.0, 0.0773178, 0.128347, 0.4556355]
driver.set_frequencies(frequencies)
driver.run(solver_type="exact", hamiltonian="rpa", spin="singlet")
for idxf, frequency in enumerate(frequencies):
print(idxf, frequency)
print("uncoupled")
diag_res = np.diag(driver.uncoupled_results[idxf])
diag_ref = np.diag(uhf_uncoupled[frequency]["result"])
diff = diag_res - diag_ref
print(diag_res)
print(diag_ref)
print(diff)
assert np.max(np.abs(diff)) < uhf_uncoupled[frequency]["error_max_diag"]
print("coupled")
diag_res = np.diag(driver.results[idxf])
diag_ref = np.diag(uhf_coupled[frequency]["result"])
diff = diag_res - diag_ref
print(diag_res)
print(diag_ref)
print(diff)
assert np.max(np.abs(diff)) < uhf_coupled[frequency]["error_max_diag"]
return
def test_explicit_uhf():
mol = molecules.molecule_water_sto3g()
mol.charge = 1
mol.spin = 1
mol.build()
mf = pyscf.scf.UHF(mol)
mf.kernel()
C = np.stack(mf.mo_coeff, axis=0)
E_a = np.diag(mf.mo_energy[0])
E_b = np.diag(mf.mo_energy[1])
assert E_a.shape == E_b.shape
E = np.stack((E_a, E_b), axis=0)
integrals_dipole_ao = mol.intor("cint1e_r_sph", comp=3)
occupations = utils.occupations_from_pyscf_mol(mol, C)
solver = iterators.ExactInv(C, E, occupations)
ao2mo = AO2MOpyscf(C, mol.verbose, mol)
ao2mo.perform_uhf_full()
solver.tei_mo = ao2mo.tei_mo
solver.tei_mo_type = "full"
driver = cphf.CPHF(solver)
operator_dipole = operators.Operator(label="dipole",
is_imaginary=False,
is_spin_dependent=False)
operator_dipole.ao_integrals = integrals_dipole_ao
driver.add_operator(operator_dipole)
driver.set_frequencies()
driver.run(solver_type="exact", hamiltonian="rpa", spin="singlet")
assert len(driver.frequencies) == len(driver.results) == 1
res = driver.results[0]
print(res)
atol = 1.0e-5
rtol = 0.0
np.testing.assert_allclose(res,
ref_water_cation_UHF_HF_STO3G,
rtol=rtol,
atol=atol)
def form_tei_mo(
self, program: Program, program_obj, tei_mo_type: AO2MOTransformationType
) -> None:
assert isinstance(program, Program)
# TODO program_obj
assert isinstance(tei_mo_type, AO2MOTransformationType)
nden = self.mocoeffs.shape[0]
assert nden in (1, 2)
if program == Program.PySCF:
from pyresponse.pyscf.ao2mo import AO2MOpyscf
ao2mo = AO2MOpyscf(self.mocoeffs, program_obj.verbose, program_obj)
elif program == Program.Psi4:
import psi4
from pyresponse.ao2mo import AO2MO
assert isinstance(program_obj, psi4.core.Molecule)
ao2mo = AO2MO(
self.mocoeffs,
self.occupations,
I=psi4.core.MintsHelper(
psi4.core.Wavefunction.build(
program_obj, psi4.core.get_global_option("BASIS")
).basisset()
)
.ao_eri()
.np,
)
else:
raise RuntimeError
if tei_mo_type == AO2MOTransformationType.partial and nden == 2:
ao2mo.perform_uhf_partial()
elif tei_mo_type == AO2MOTransformationType.partial and nden == 1:
ao2mo.perform_rhf_partial()
elif tei_mo_type == AO2MOTransformationType.full and nden == 2:
ao2mo.perform_uhf_full()
elif tei_mo_type == AO2MOTransformationType.full and nden == 1:
ao2mo.perform_rhf_full()
else:
raise ValueError(f"Unknown combination of tei_mo_type {tei_mo_type} and nden {nden}")
self.tei_mo = ao2mo.tei_mo
self.tei_mo_type = tei_mo_type
def form_tei_mo(self, program, program_obj, tei_mo_type="partial"):
assert tei_mo_type in ("partial", "full")
nden = self.mocoeffs.shape[0]
assert nden in (1, 2)
if program == Program.PySCF:
from pyresponse.pyscf.ao2mo import AO2MOpyscf
ao2mo = AO2MOpyscf(self.mocoeffs, program_obj.verbose, program_obj)
elif program == Program.Psi4:
from pyresponse.ao2mo import AO2MO
import psi4
assert isinstance(program_obj, psi4.core.Molecule)
ao2mo = AO2MO(
self.mocoeffs,
self.occupations,
I=psi4.core.MintsHelper(
psi4.core.Wavefunction.build(
program_obj, psi4.core.get_global_option(
"BASIS")).basisset()).ao_eri().np,
)
else:
raise RuntimeError
if tei_mo_type == "partial" and nden == 2:
ao2mo.perform_uhf_partial()
elif tei_mo_type == "partial" and nden == 1:
ao2mo.perform_rhf_partial()
elif tei_mo_type == "full" and nden == 2:
ao2mo.perform_uhf_full()
elif tei_mo_type == "full" and nden == 1:
ao2mo.perform_rhf_full()
else:
# TODO more specific exception
raise Exception
self.tei_mo = ao2mo.tei_mo
self.tei_mo_type = tei_mo_type
def test_explicit_uhf_outside_solver():
mol = molecules.molecule_water_sto3g()
mol.charge = 1
mol.spin = 1
mol.build()
mf = pyscf.scf.UHF(mol)
mf.kernel()
C_a = mf.mo_coeff[0]
C_b = mf.mo_coeff[1]
E_a = np.diag(mf.mo_energy[0])
E_b = np.diag(mf.mo_energy[1])
assert C_a.shape == C_b.shape
assert E_a.shape == E_b.shape
ao2mo = AO2MOpyscf(mf.mo_coeff, 5, mol)
ao2mo.perform_uhf_full()
tei_mo_aaaa, tei_mo_aabb, tei_mo_bbaa, tei_mo_bbbb = ao2mo.tei_mo
occupations = utils.occupations_from_pyscf_mol(mol, mf.mo_coeff)
nocc_a, nvirt_a, nocc_b, nvirt_b = occupations
A_s_ss_a = eqns.form_rpa_a_matrix_mo_singlet_ss_full(E_a, tei_mo_aaaa, nocc_a)
A_s_os_a = eqns.form_rpa_a_matrix_mo_singlet_os_full(tei_mo_aabb, nocc_a, nocc_b)
B_s_ss_a = eqns.form_rpa_b_matrix_mo_singlet_ss_full(tei_mo_aaaa, nocc_a)
B_s_os_a = eqns.form_rpa_b_matrix_mo_singlet_os_full(tei_mo_aabb, nocc_a, nocc_b)
A_s_ss_b = eqns.form_rpa_a_matrix_mo_singlet_ss_full(E_b, tei_mo_bbbb, nocc_b)
A_s_os_b = eqns.form_rpa_a_matrix_mo_singlet_os_full(tei_mo_bbaa, nocc_b, nocc_a)
B_s_ss_b = eqns.form_rpa_b_matrix_mo_singlet_ss_full(tei_mo_bbbb, nocc_b)
B_s_os_b = eqns.form_rpa_b_matrix_mo_singlet_os_full(tei_mo_bbaa, nocc_b, nocc_a)
# Since the "triplet" part contains no Coulomb contribution, and
# (xx|yy) is only in the Coulomb part, there is no ss/os
# separation for the triplet part.
G_aa = np.block([[A_s_ss_a, B_s_ss_a], [B_s_ss_a, A_s_ss_a]])
G_bb = np.block([[A_s_ss_b, B_s_ss_b], [B_s_ss_b, A_s_ss_b]])
G_ab = np.block([[A_s_os_a, B_s_os_a], [B_s_os_a, A_s_os_a]])
G_ba = np.block([[A_s_os_b, B_s_os_b], [B_s_os_b, A_s_os_b]])
G_aa_inv = np.linalg.inv(G_aa)
G_bb_inv = np.linalg.inv(G_bb)
nov_aa = nocc_a * nvirt_a
nov_bb = nocc_b * nvirt_b
assert G_aa_inv.shape == (2 * nov_aa, 2 * nov_aa)
assert G_bb_inv.shape == (2 * nov_bb, 2 * nov_bb)
# Form the operator-independent part of the response vectors.
left_a = np.linalg.inv(G_aa - np.dot(G_ab, np.dot(G_bb_inv, G_ba)))
left_b = np.linalg.inv(G_bb - np.dot(G_ba, np.dot(G_aa_inv, G_ab)))
integrals_dipole_ao = mol.intor("cint1e_r_sph", comp=3)
integrals_dipole_mo_ai_a = []
integrals_dipole_mo_ai_b = []
for comp in range(3):
integrals_dipole_mo_ai_comp_a = np.dot(
C_a[:, nocc_a:].T, np.dot(integrals_dipole_ao[comp, ...], C_a[:, :nocc_a])
)
integrals_dipole_mo_ai_comp_b = np.dot(
C_b[:, nocc_b:].T, np.dot(integrals_dipole_ao[comp, ...], C_b[:, :nocc_b])
)
integrals_dipole_mo_ai_comp_a = np.reshape(integrals_dipole_mo_ai_comp_a, -1, order="F")
integrals_dipole_mo_ai_comp_b = np.reshape(integrals_dipole_mo_ai_comp_b, -1, order="F")
integrals_dipole_mo_ai_a.append(integrals_dipole_mo_ai_comp_a)
integrals_dipole_mo_ai_b.append(integrals_dipole_mo_ai_comp_b)
integrals_dipole_mo_ai_a = np.stack(integrals_dipole_mo_ai_a, axis=0).T
integrals_dipole_mo_ai_b = np.stack(integrals_dipole_mo_ai_b, axis=0).T
integrals_dipole_mo_ai_a_super = np.concatenate(
(integrals_dipole_mo_ai_a, -integrals_dipole_mo_ai_a), axis=0
)
integrals_dipole_mo_ai_b_super = np.concatenate(
(integrals_dipole_mo_ai_b, -integrals_dipole_mo_ai_b), axis=0
)
# Form the operator-dependent part of the response vectors.
right_a = integrals_dipole_mo_ai_a_super - (
np.dot(G_ab, np.dot(G_bb_inv, integrals_dipole_mo_ai_b_super))
)
right_b = integrals_dipole_mo_ai_b_super - (
np.dot(G_ba, np.dot(G_aa_inv, integrals_dipole_mo_ai_a_super))
)
# The total response vector for each spin is the product of the
# operator-independent (left) and operator-dependent (right)
# parts.
rspvec_a = np.dot(left_a, right_a)
rspvec_b = np.dot(left_b, right_b)
res_a = np.dot(integrals_dipole_mo_ai_a_super.T, rspvec_a) / 2
res_b = np.dot(integrals_dipole_mo_ai_b_super.T, rspvec_b) / 2
res_u = 2 * (res_a + res_b)
print(res_u)
atol = 1.0e-5
rtol = 0.0
np.testing.assert_allclose(res_u, ref_water_cation_UHF_HF_STO3G, rtol=rtol, atol=atol)
def test_explicit_uhf_from_rhf_outside_solver():
mol = molecules.molecule_water_sto3g()
mol.build()
mf = pyscf.scf.RHF(mol)
mf.kernel()
mocoeffs = mf.mo_coeff
moenergies = mf.mo_energy
ao2mo = AO2MOpyscf(mocoeffs, mol.verbose, mol)
ao2mo.perform_rhf_full()
tei_mo = ao2mo.tei_mo[0]
C_a = mocoeffs
C_b = C_a.copy()
E_a = np.diag(moenergies)
# E_b = E_a.copy()
occupations = utils.occupations_from_pyscf_mol(mol, mocoeffs)
nocc_a, nvirt_a, nocc_b, nvirt_b = occupations
# Same-spin and opposite-spin contributions should add together
# properly for restricted wavefunction.
A_s = eqns.form_rpa_a_matrix_mo_singlet_full(E_a, tei_mo, nocc_a)
A_s_ss = eqns.form_rpa_a_matrix_mo_singlet_ss_full(E_a, tei_mo, nocc_a)
A_s_os = eqns.form_rpa_a_matrix_mo_singlet_os_full(tei_mo, nocc_a, nocc_b)
np.testing.assert_allclose(A_s, A_s_ss + A_s_os)
B_s = eqns.form_rpa_b_matrix_mo_singlet_full(tei_mo, nocc_a)
B_s_ss = eqns.form_rpa_b_matrix_mo_singlet_ss_full(tei_mo, nocc_a)
B_s_os = eqns.form_rpa_b_matrix_mo_singlet_os_full(tei_mo, nocc_a, nocc_b)
np.testing.assert_allclose(B_s, B_s_ss + B_s_os)
# Since the "triplet" part contains no Coulomb contribution, and
# (xx|yy) is only in the Coulomb part, there is no ss/os
# separation for the triplet part.
G_r = np.block([[A_s, B_s], [B_s, A_s]])
G_aa = np.block([[A_s_ss, B_s_ss], [B_s_ss, A_s_ss]])
G_bb = G_aa.copy()
G_ab = np.block([[A_s_os, B_s_os], [B_s_os, A_s_os]])
G_ba = G_ab.copy()
np.testing.assert_allclose(G_r, (G_aa + G_ab))
G_r_inv = np.linalg.inv(G_r)
G_aa_inv = np.linalg.inv(G_aa)
G_bb_inv = np.linalg.inv(G_bb)
assert G_r_inv.shape == (2 * nocc_a * nvirt_a, 2 * nocc_a * nvirt_a)
assert G_aa_inv.shape == (2 * nocc_a * nvirt_a, 2 * nocc_a * nvirt_a)
assert G_bb_inv.shape == (2 * nocc_b * nvirt_b, 2 * nocc_b * nvirt_b)
# Form the operator-independent part of the response vectors.
left_alph = np.linalg.inv(G_aa - np.dot(G_ab, np.dot(G_bb_inv, G_ba)))
left_beta = np.linalg.inv(G_bb - np.dot(G_ba, np.dot(G_aa_inv, G_ab)))
integrals_dipole_ao = mol.intor("cint1e_r_sph", comp=3)
integrals_dipole_mo_ai_r = []
integrals_dipole_mo_ai_a = []
integrals_dipole_mo_ai_b = []
for comp in range(3):
integrals_dipole_mo_ai_comp_r = np.dot(
C_a[:, nocc_a:].T, np.dot(integrals_dipole_ao[comp, ...], C_a[:, :nocc_a])
)
integrals_dipole_mo_ai_comp_a = np.dot(
C_a[:, nocc_a:].T, np.dot(integrals_dipole_ao[comp, ...], C_a[:, :nocc_a])
)
integrals_dipole_mo_ai_comp_b = np.dot(
C_b[:, nocc_b:].T, np.dot(integrals_dipole_ao[comp, ...], C_b[:, :nocc_b])
)
integrals_dipole_mo_ai_comp_r = np.reshape(integrals_dipole_mo_ai_comp_r, -1, order="F")
integrals_dipole_mo_ai_comp_a = np.reshape(integrals_dipole_mo_ai_comp_a, -1, order="F")
integrals_dipole_mo_ai_comp_b = np.reshape(integrals_dipole_mo_ai_comp_b, -1, order="F")
integrals_dipole_mo_ai_r.append(integrals_dipole_mo_ai_comp_r)
integrals_dipole_mo_ai_a.append(integrals_dipole_mo_ai_comp_a)
integrals_dipole_mo_ai_b.append(integrals_dipole_mo_ai_comp_b)
integrals_dipole_mo_ai_r = np.stack(integrals_dipole_mo_ai_r, axis=0).T
integrals_dipole_mo_ai_a = np.stack(integrals_dipole_mo_ai_a, axis=0).T
integrals_dipole_mo_ai_b = np.stack(integrals_dipole_mo_ai_b, axis=0).T
integrals_dipole_mo_ai_r_super = np.concatenate(
(integrals_dipole_mo_ai_r, -integrals_dipole_mo_ai_r), axis=0
)
integrals_dipole_mo_ai_a_super = np.concatenate(
(integrals_dipole_mo_ai_a, -integrals_dipole_mo_ai_a), axis=0
)
integrals_dipole_mo_ai_b_super = np.concatenate(
(integrals_dipole_mo_ai_b, -integrals_dipole_mo_ai_b), axis=0
)
# Form the operator-dependent part of the response vectors.
right_alph = integrals_dipole_mo_ai_a_super - (
np.dot(G_ab, np.dot(G_bb_inv, integrals_dipole_mo_ai_b_super))
)
right_beta = integrals_dipole_mo_ai_b_super - (
np.dot(G_ba, np.dot(G_aa_inv, integrals_dipole_mo_ai_a_super))
)
rspvec_r = np.dot(G_r_inv, integrals_dipole_mo_ai_r_super)
# The total response vector for each spin is the product of the
# operator-independent (left) and operator-dependent (right)
# parts.
rspvec_a = np.dot(left_alph, right_alph)
rspvec_b = np.dot(left_beta, right_beta)
res_r = 4 * np.dot(integrals_dipole_mo_ai_r_super.T, rspvec_r) / 2
res_a = np.dot(integrals_dipole_mo_ai_a_super.T, rspvec_a) / 2
res_b = np.dot(integrals_dipole_mo_ai_b_super.T, rspvec_b) / 2
res_u = 2 * (res_a + res_b)
atol = 1.0e-8
rtol = 0.0
np.testing.assert_allclose(res_u, res_r, rtol=rtol, atol=atol)
print(res_r)
print(res_u)
def test_HF_both_singlet_HF_STO3G():
mol = pyscf.gto.Mole()
mol.verbose = 0
mol.output = None
# pylint: disable=bad-whitespace
mol.atom = [["H", (0.0, 0.0, 0.917)], ["F", (0.0, 0.0, 0.0)]]
mol.basis = "sto-3g"
mol.build()
mf = pyscf.scf.RHF(mol)
mf.scf()
C = utils.fix_mocoeffs_shape(mf.mo_coeff)
E = utils.fix_moenergies_shape(mf.mo_energy)
occupations = utils.occupations_from_pyscf_mol(mol, C)
solver_tda = iterators.ExactDiagonalizationSolverTDA(C, E, occupations)
solver_tdhf = iterators.ExactDiagonalizationSolver(C, E, occupations)
ao2mo = AO2MOpyscf(C, mol.verbose, mol)
ao2mo.perform_rhf_partial()
tei_mo = ao2mo.tei_mo
solver_tda.tei_mo = tei_mo
solver_tda.tei_mo_type = "partial"
solver_tdhf.tei_mo = tei_mo
solver_tdhf.tei_mo_type = "partial"
driver_tda = td.TDA(solver_tda)
driver_tdhf = td.TDHF(solver_tdhf)
nroots = 5
print("TDA using TDA()")
driver_tda.run(solver_type="exact", hamiltonian="tda", spin="singlet")
excitation_energies_tda_using_tda = driver_tda.solver.eigvals[:nroots].real
print("TDA using TDHF()")
driver_tdhf.run(solver_type="exact", hamiltonian="tda", spin="singlet")
excitation_energies_tda_using_tdhf = driver_tdhf.solver.eigvals[:nroots].real
print("RPA using TDHF()")
driver_tdhf.run(solver_type="exact", hamiltonian="rpa", spin="singlet")
excitation_energies_rpa = driver_tdhf.solver.eigvals[:nroots].real
assert (
excitation_energies_tda_using_tda.shape
== excitation_energies_tda_using_tdhf.shape
)
assert excitation_energies_tda_using_tdhf.shape == excitation_energies_rpa.shape
# There should be no difference in the TDA results regardless of
# which implementation used.
assert (
excitation_energies_tda_using_tda - excitation_energies_tda_using_tdhf
).all() == 0
# Now compare against reference_data
ref_tda = HF_neutral_singlet_HF_STO3G_CIS_qchem
ref_rpa = HF_neutral_singlet_HF_STO3G_RPA_qchem
thresh = 1.0e-7
for i in range(nroots):
abs_diff = abs(ref_tda["etenergies"][i] - excitation_energies_tda_using_tda[i])
assert abs_diff < thresh
thresh = 1.0e-7
for i in range(nroots):
abs_diff = abs(ref_rpa["etenergies"][i] - excitation_energies_rpa[i])
assert abs_diff < thresh
return
def calculate_uhf(
dalton_tmpdir: Path,
hamiltonian: str,
spin: str,
operator_label: str,
operator: str,
source_moenergies: str,
source_mocoeffs: str,
source_operator: str,
):
if operator_label:
# TODO add dipvel
assert operator_label in ("dipole", "angmom", "spinorb")
assert source_moenergies in ("pyscf", "dalton")
assert source_mocoeffs in ("pyscf", "dalton")
dalton_molecule = dalmol.readin(dalton_tmpdir / "DALTON.BAS")
lines = []
for atom in dalton_molecule:
label = atom["label"][0]
center = atom["center"][0]
center_str = " ".join(["{:f}".format(pos) for pos in center])
line = "{:3} {}".format(label, center_str)
lines.append(line)
lines = "\n".join(lines)
# PySCF molecule setup, needed for generating the TEIs in the MO
# basis.
mol = pyscf.gto.Mole()
verbose = 1
mol.verbose = verbose
mol.atom = lines
mol.unit = "Bohr"
# TODO read basis from DALTON molecule
mol.basis = "sto-3g"
mol.symmetry = False
# TODO read charge from DALTON molecule?
mol.charge = 1
# TODO read spin from DALTON molecule?
mol.spin = 1
mol.build()
ifc = sirifc.sirifc(dalton_tmpdir / "SIRIFC")
occupations = utils.occupations_from_sirifc(ifc)
if source_moenergies == "pyscf" or source_mocoeffs == "pyscf":
mf = pyscf.scf.UHF(mol)
mf.kernel()
if source_moenergies == "pyscf":
E_alph = np.diag(mf.mo_energy[0])
E_beta = np.diag(mf.mo_energy[1])
E = np.stack((E_alph, E_beta), axis=0)
elif source_moenergies == "dalton":
job = ccopen(dalton_tmpdir / "DALTON.OUT")
data = job.parse()
# pylint: disable=no-member
E = np.diag([
convertor(x, "eV", "hartree") for x in data.moenergies[0]
])[np.newaxis, ...]
E = np.concatenate((E, E), axis=0)
else:
pass
if source_mocoeffs == "pyscf":
C = mf.mo_coeff
elif source_mocoeffs == "dalton":
C = ifc.cmo[0][np.newaxis, ...]
C = np.concatenate((C, C), axis=0)
else:
pass
solver = solvers.ExactInv(C, E, occupations)
solver.tei_mo = AO2MOpyscf(mol, C).perform_uhf_partial()
solver.tei_mo_type = AO2MOTransformationType.partial
driver = cphf.CPHF(solver)
if operator:
driver.add_operator(operator)
elif operator_label:
if operator_label == "dipole":
operator_dipole = operators.Operator(label="dipole",
is_imaginary=False,
is_spin_dependent=False,
triplet=False)
integrals_dipole_ao = mol.intor("cint1e_r_sph", comp=3)
operator_dipole.ao_integrals = integrals_dipole_ao
driver.add_operator(operator_dipole)
elif operator_label == "angmom":
operator_angmom = operators.Operator(label="angmom",
is_imaginary=True,
is_spin_dependent=False,
triplet=False)
integrals_angmom_ao = mol.intor("cint1e_cg_irxp_sph", comp=3)
operator_angmom.ao_integrals = integrals_angmom_ao
driver.add_operator(operator_angmom)
elif operator_label == "spinorb":
operator_spinorb = operators.Operator(label="spinorb",
is_imaginary=True,
is_spin_dependent=False,
triplet=False)
integrals_spinorb_ao = 0
for atm_id in range(mol.natm):
mol.set_rinv_orig(mol.atom_coord(atm_id))
chg = mol.atom_charge(atm_id)
integrals_spinorb_ao += chg * mol.intor("cint1e_prinvxp_sph",
comp=3)
operator_spinorb.ao_integrals = integrals_spinorb_ao
driver.add_operator(operator_spinorb)
else:
pass
else:
pass
driver.set_frequencies()
driver.run(hamiltonian=Hamiltonian[hamiltonian.upper()], spin=Spin[spin])
return driver.results[0]