Electronic Structure Stack Refactoring - Part 2

.pylintdict

@@ -1,3 +1,4 @@
+aa
 acknowledgment
 adjoint
 aer
@@ -22,8 +23,8 @@ antisymmetric
 antisymmetrized
 ao
 april
-arginine
 arg
+arginine
 args
 arrowheads
 arrowstyle
@@ -145,6 +146,7 @@ eigenvector
 eigenvectors
 einact
 einsum
+electronicintegrals
 endian
 endif
 enum
@@ -207,7 +209,7 @@ hijkls
 hijs
 hilbert
 histidine
-HJO
+hjo
 html
 https
 hubbard
@@ -217,7 +219,10 @@ ifdef
 ifortvars
 ij
 ijkl
+ijlk
 ik
+iklj
+il
 init
 initializer
 initio
@@ -248,6 +253,7 @@ jcf
 jcp
 jernigan
 ji
+jk
 jl
 jordan
 jørgensen
@@ -266,12 +272,12 @@ kwargs
 kwds
 labelled
 lda
-leighton
-lexicographically
 ldots
+leighton
 len
 leucine
 levinthal
+lexicographically
 libifcoremd
 libor
 libxc
@@ -288,6 +294,7 @@ lysine
 macos
 majorana
 makefile
+matmul
 matplotlib
 maxdepth
 maxiter
@@ -330,10 +337,10 @@ nbasis
 nd
 ndarray
 nelec
-neutron
 neq
 networkx
 neuropeptide
+neutron
 nicholas
 nielsen
 nisq
@@ -357,8 +364,8 @@ ok
 ollitrault
 onee
 oneeints
-onwards
 onsite
+onwards
 opflow
 oppenheimer
 optimizers
@@ -382,15 +389,16 @@ perturbative
 pes
 phenylalanine
 phonons
-physrevd
 physik
+physrevd
 plesset
 pmatrix
 polynomialtensor
 polypeptides
 popovas
 pos
 posteriori
+pqrs
 pre
 prebuilt
 prepend
@@ -400,6 +408,7 @@ preprocesses
 proline
 protium
 proton
+prsq
 ps
 pseudorandom
 pxd
@@ -410,17 +419,19 @@ qarg
 qargs
 qasm
 qbit
+qc
 qcbase
 qcmatrixio
 qcschema
 qeom
 qfi
 qiskit
 qiskit's
-qc
+qj
 qmolecule
 qn
 qregs
+qs
 quantization
 quantized
 quartic
@@ -446,6 +457,7 @@ rgb
 rgba
 rhf
 rhs
+rk
 robert
 rohf
 rossmannek
@@ -475,8 +487,9 @@ setted
 shende
 siddhartha
 sklearn
-soham
+sl
 slater
+soham
 sparselabelop
 spinop
 springer

qiskit_nature/second_q/algorithms/initial_points/hf_initial_point.py

@@ -82,7 +82,7 @@ def grouped_property(self, grouped_property: BaseProblem) -> None:
             )
             return
 
-        self._reference_energy = electronic_energy.reference_energy if not None else 0.0
+        self._reference_energy = grouped_property.reference_energy if not None else 0.0
         self._grouped_property = grouped_property
 
     def to_numpy_array(self) -> np.ndarray:

qiskit_nature/second_q/algorithms/initial_points/mp2_initial_point.py

@@ -18,9 +18,9 @@
 
 from qiskit_nature.exceptions import QiskitNatureError
 from qiskit_nature.second_q.circuit.library import UCC
+from qiskit_nature.second_q.operators import ElectronicIntegrals
+from qiskit_nature.second_q.operators.tensor_ordering import _phys_to_chem
 from qiskit_nature.second_q.problems import BaseProblem, ElectronicStructureProblem
-from qiskit_nature.second_q.properties.bases import ElectronicBasis
-from qiskit_nature.second_q.properties.integrals import ElectronicIntegrals
 
 
 from .initial_point import InitialPoint
@@ -158,29 +158,28 @@ def grouped_property(self, grouped_property: BaseProblem) -> None:
                 "The `ElectronicEnergy` cannot be obtained from the `grouped_property`."
             )
 
-        two_body_mo_integral: ElectronicIntegrals | None = (
-            electronic_energy.get_electronic_integral(ElectronicBasis.MO, 2)
-        )
-        if two_body_mo_integral is None:
+        two_body_mo_integral: ElectronicIntegrals = electronic_energy.electronic_integrals.two_body
+        if two_body_mo_integral.alpha.is_empty():
             raise QiskitNatureError(
-                "The two-body MO `electronic_integrals` cannot be obtained from the `grouped_property`."
+                "The alpha-alpha spin two-body MO `electronic_integrals` cannot be empty."
             )
 
-        orbital_energies: np.ndarray | None = electronic_energy.orbital_energies
+        orbital_energies: np.ndarray | None = grouped_property.orbital_energies
         if orbital_energies is None:
             raise QiskitNatureError(
                 "The `orbital_energies` cannot be obtained from the `grouped_property`."
             )
 
-        integral_matrix: np.ndarray = two_body_mo_integral.get_matrix()
-        if not np.allclose(integral_matrix, two_body_mo_integral.get_matrix(2)):
+        if two_body_mo_integral.beta.get("++--", None) is not None:
             raise NotImplementedError(
                 "`MP2InitialPoint` only supports restricted-spin setups. "
                 "Alpha and beta spin orbitals must be identical. "
                 "See https://github.com/Qiskit/qiskit-nature/issues/645."
             )
 
-        reference_energy = electronic_energy.reference_energy if not None else 0.0
+        integral_matrix = _phys_to_chem(two_body_mo_integral.alpha.get("++--"))
+
+        reference_energy = grouped_property.reference_energy if not None else 0.0
 
         particle_number = grouped_property.properties.particle_number
         if particle_number is None:

qiskit_nature/second_q/drivers/electronic_structure_driver.py

@@ -32,6 +32,7 @@
     QCWavefunction,
 )
 from qiskit_nature.second_q.problems import ElectronicStructureProblem
+from qiskit_nature.second_q.properties.bases import ElectronicBasis
 
 from .base_driver import BaseDriver
 
@@ -112,12 +113,14 @@ def to_qcschema(self) -> QCSchema:
     def to_problem(
         self,
         *,
+        basis: ElectronicBasis = ElectronicBasis.MO,
         include_dipole: bool = True,
     ) -> ElectronicStructureProblem:
         """Extends the :meth:`to_qcschema` method and translates the :class:`.QCSchema` object to an
         :class:`.ElectronicStructureProblem`.
 
         Args:
+            basis: the :class:`.ElectronicBasis` in which to construct the problem.
             include_dipole: whether or not to include an :class:`.ElectronicDipoleMoment` property
                 in the generated problem (if the data is available).
 

qiskit_nature/second_q/drivers/gaussiand/gaussiandriver.py

@@ -31,11 +31,14 @@
 from qiskit_nature.settings import settings
 from qiskit_nature.second_q.formats.molecule_info import MoleculeInfo
 from qiskit_nature.second_q.formats.qcschema import QCSchema
-from qiskit_nature.second_q.formats.qcschema_translator import qcschema_to_problem
+from qiskit_nature.second_q.formats.qcschema_translator import (
+    qcschema_to_problem,
+    get_ao_to_mo_from_qcschema,
+)
+from qiskit_nature.second_q.operators import ElectronicIntegrals
 from qiskit_nature.second_q.problems import ElectronicStructureProblem
-from qiskit_nature.second_q.properties import DipoleMoment, ElectronicDipoleMoment
+from qiskit_nature.second_q.properties import ElectronicDipoleMoment
 from qiskit_nature.second_q.properties.bases import ElectronicBasis
-from qiskit_nature.second_q.properties.integrals import OneBodyElectronicIntegrals
 
 from .gaussian_utils import run_g16
 from ..electronic_structure_driver import ElectronicStructureDriver, MethodType, _QCSchemaData
@@ -409,46 +412,49 @@ def _qcschema_from_matrix_file(mel: MatEl) -> QCSchema:
     def to_problem(
         self,
         *,
+        basis: ElectronicBasis = ElectronicBasis.MO,
         include_dipole: bool = True,
     ) -> ElectronicStructureProblem:
-        return GaussianDriver._problem_from_matrix_file(self._mel, include_dipole=include_dipole)
+        return GaussianDriver._problem_from_matrix_file(
+            self._mel, basis=basis, include_dipole=include_dipole
+        )
 
     @staticmethod
     def _problem_from_matrix_file(
-        mel: MatEl, *, include_dipole: bool = True
+        mel: MatEl,
+        *,
+        basis: ElectronicBasis = ElectronicBasis.MO,
+        include_dipole: bool = True,
     ) -> ElectronicStructureProblem:
         qcschema = GaussianDriver._qcschema_from_matrix_file(mel)
 
-        problem = qcschema_to_problem(qcschema)
+        problem = qcschema_to_problem(qcschema, basis=basis)
 
         if include_dipole:
             # dipole moment
             dipints = GaussianDriver._get_matrix(mel, "DIPOLE INTEGRALS")
             dipints = np.einsum("ijk->kji", dipints)
 
-            x_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (dipints[0], None))
-            y_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (dipints[1], None))
-            z_dip_ints = OneBodyElectronicIntegrals(ElectronicBasis.AO, (dipints[2], None))
+            x_dip = ElectronicIntegrals.from_raw_integrals(dipints[0])
+            y_dip = ElectronicIntegrals.from_raw_integrals(dipints[1])
+            z_dip = ElectronicIntegrals.from_raw_integrals(dipints[2])
 
-            x_dipole = DipoleMoment(
-                "x", [x_dip_ints, x_dip_ints.transform_basis(problem.basis_transform)]
-            )
-            y_dipole = DipoleMoment(
-                "y", [y_dip_ints, y_dip_ints.transform_basis(problem.basis_transform)]
-            )
-            z_dipole = DipoleMoment(
-                "z", [z_dip_ints, z_dip_ints.transform_basis(problem.basis_transform)]
-            )
+            if basis == ElectronicBasis.MO:
+                basis_transform = get_ao_to_mo_from_qcschema(qcschema)
+
+                x_dip = basis_transform.transform_electronic_integrals(x_dip)
+                y_dip = basis_transform.transform_electronic_integrals(y_dip)
+                z_dip = basis_transform.transform_electronic_integrals(z_dip)
 
             coords = np.reshape(mel.c, (len(mel.ian), 3))
             nucl_dip = np.einsum("i,ix->x", mel.ian, coords)
             nucl_dip = np.round(nucl_dip, decimals=8)
 
-            problem.properties.electronic_dipole_moment = ElectronicDipoleMoment(
-                [x_dipole, y_dipole, z_dipole],
-                nuclear_dipole_moment=nucl_dip,
-                reverse_dipole_sign=True,
-            )
+            dipole_moment = ElectronicDipoleMoment(x_dip, y_dip, z_dip)
+            dipole_moment.nuclear_dipole_moment = nucl_dip
+            dipole_moment.reverse_dipole_sign = True
+
+            problem.properties.electronic_dipole_moment = dipole_moment
 
         return problem