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changed default basis, added ecp option #156

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merged 6 commits into from
May 27, 2022
Merged

changed default basis, added ecp option #156

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fd360c5
changed default basis, added ecp option
JamesB-1qbit May 24, 2022
1cc6a7e
response to PR
JamesB-1qbit May 25, 2022
54e2181
change default ecp to immutable None
JamesB-1qbit May 25, 2022
ed5226c
added test
JamesB-1qbit May 26, 2022
88c5b1d
changed initialization of ecp
JamesB-1qbit May 26, 2022
1f05973
fixed test
JamesB-1qbit May 26, 2022
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2 changes: 1 addition & 1 deletion tangelo/toolboxes/molecular_computation/frozen_orbitals.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def get_frozen_core(molecule):

# Counting how many of each element is in the molecule.
elements = {i: molecule.elements.count(i) for i in molecule.elements}
frozen_core = sum([v * core_orbitals[k] for k, v in elements.items()])
frozen_core = sum([v * core_orbitals.get(k, 0) for k, v in elements.items()])

return frozen_core

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20 changes: 14 additions & 6 deletions tangelo/toolboxes/molecular_computation/molecule.py
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Expand Up @@ -94,7 +94,7 @@ class Molecule:
n_min_orbitals: int = field(init=False)

def __post_init__(self):
mol = self.to_pyscf(basis="sto-3g", symmetry=False)
mol = self.to_pyscf()
self.n_atoms = mol.natm
self.n_electrons = mol.nelectron
self.n_min_orbitals = mol.nao_nr()
Expand All @@ -107,21 +107,26 @@ def elements(self):
def coords(self):
return np.array([self.xyz[i][1] for i in range(self.n_atoms)])

def to_pyscf(self, basis="sto-3g", symmetry=False):
def to_pyscf(self, basis="CRENBL", symmetry=False, ecp=None):
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"""Method to return a pyscf.gto.Mole object.

Args:
basis (string): Basis set.
symmetry (bool): Flag to turn symmetry on
ecp (dict): Dictionary with ecp definition for each atom e.g. {"Cu": "crenbl"}

Returns:
pyscf.gto.Mole: PySCF compatible object.
"""
if ecp is None:
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ecp = dict()

mol = gto.Mole(atom=self.xyz)
mol.basis = basis
mol.charge = self.q
mol.spin = self.spin
mol.symmetry = symmetry
mol.ecp = ecp
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mol.build()

self.xyz = list()
Expand All @@ -137,7 +142,7 @@ def to_file(self, filename, format=None):
filename (str): The name of the file to output the geometry.
format (str): The output type of "raw", "xyz", or "zmat". If None, will be inferred by the filename
"""
mol = self.to_pyscf(basis="sto-3g")
mol = self.to_pyscf()
mol.tofile(filename, format)

def to_openfermion(self, basis="sto-3g"):
Expand All @@ -161,6 +166,8 @@ class SecondQuantizedMolecule(Molecule):

Attributes:
basis (string): Basis set.
ecp (dict): The effective core potential (ecp) for any atoms in the molecule.
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e.g. {"C": "crenbl"} use CRENBL ecp for Carbon atoms.
symmetry (bool or str): Whether to use symmetry in RHF or ROHF calculation.
Can also specify point group using pyscf allowed string.
e.g. "Dooh", "D2h", "C2v", ...
Expand Down Expand Up @@ -195,6 +202,7 @@ class SecondQuantizedMolecule(Molecule):
actives_mos (list): Active MOs indexes.
"""
basis: str = "sto-3g"
ecp: dict = field(default_factory=dict)
symmetry: bool = False
frozen_orbitals: list or int = field(default="frozen_core", repr=False)

Expand Down Expand Up @@ -273,7 +281,7 @@ def _compute_mean_field(self):
(mf_energy, mo_energies, mo_occ, n_mos and n_sos).
"""

molecule = self.to_pyscf(self.basis, self.symmetry)
molecule = self.to_pyscf(self.basis, self.symmetry, self.ecp)

self.mean_field = scf.RHF(molecule)
self.mean_field.verbose = 0
Expand Down Expand Up @@ -331,7 +339,7 @@ def _convert_frozen_orbitals(self, frozen_orbitals):
virtual and frozen virtual orbital indexes.
"""

if frozen_orbitals == "frozen_core":
if frozen_orbitals == "frozen_core" and not self.ecp:
frozen_orbitals = get_frozen_core(self.to_pyscf(self.basis))
elif frozen_orbitals is None:
frozen_orbitals = 0
Expand Down Expand Up @@ -456,7 +464,7 @@ def get_integrals(self, mo_coeff=None, consider_frozen=True):
"""

# Pyscf molecule to get integrals.
pyscf_mol = self.to_pyscf(self.basis, self.symmetry)
pyscf_mol = self.to_pyscf(self.basis, self.symmetry, self.ecp)
if mo_coeff is None:
mo_coeff = self.mean_field.mo_coeff

Expand Down