def get_basis_info(self):
""" Obtain basis set info from DALTON.BAS """
molecule = mol.readin(self.dalton_bas)
self.cpa = mol.contracted_per_atom(molecule)
self.cpa_l = mol.contracted_per_atom_l(molecule)
self.opa = mol.occupied_per_atom(molecule)
self.noa = len(self.opa)
#
# Total number of basis functions and occpied orbitals
#
self.nbf = sum(self.cpa)
self.noc = 0
for o in self.opa:
self.noc += len(o)
def get_basis_info(self):
""" Obtain basis set info from DALTON.BAS """
molecule = mol.readin(self.dalton_bas)
self.cpa = mol.contracted_per_atom(molecule)
self.cpa_l = mol.contracted_per_atom_l(molecule)
self.opa = mol.occupied_per_atom(molecule)
self.noa = len(self.opa)
#
# Total number of basis functions and occupied orbitals
#
self.nbf = sum(self.cpa)
self.noc = 0
for o in self.opa:
self.noc += len(o)
def set_cfunc(bf):
"""Return a list of contracted AO function objects
"""
from daltools import mol
molecule = mol.readin(bf)
cfunc = []
for atom in molecule:
for center in atom['center']:
for l, lblock in enumerate(atom['basis']):
for block in lblock:
#pe = np.array(block['prim'])
pe = block['prim']
cc = np.array(block['cont'])
for c in range(cc.shape[1]):
cfunc.append(
generate_contracted(l, pe, cc[:, c], center))
return cfunc
def setup(self):
self.tmpdir = tmpdir(__file__)
dalton_bas = self.tmpdir/"DALTON.BAS"
self.bas = mol.readin(dalton_bas)
self.maxDiff = None
def calculate_uhf(
dalton_tmpdir,
hamiltonian=None,
spin=None,
operator_label=None,
operator=None,
source_moenergies=None,
source_mocoeffs=None,
source_operator=None,
):
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 = iterators.ExactInv(C, E, occupations)
solver.tei_mo = ao2mo.perform_tei_ao2mo_uhf_partial(mol, C)
solver.tei_mo_type = "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(solver_type="exact", hamiltonian=hamiltonian, spin=spin)
return driver.results[0]