[WIP] Refactor Chemistry Drivers to also accept Molecule class (#1297)

* Refactor Chemistry Drivers

* add some setters to molecule

* FermionicDriver & BaseDriver properties

* Updated docstrings

* Perturbation support plus unit test case

Co-authored-by: woodsp <woodsp@us.ibm.com>

qiskit/chemistry/applications/molecular_ground_state_energy.py

@@ -24,14 +24,14 @@
 from qiskit.chemistry.components.variational_forms import UCCSD
 from qiskit.chemistry.core import (Hamiltonian, TransformationType, QubitMappingType,
                                    ChemistryOperator, MolecularGroundStateResult)
-from qiskit.chemistry.drivers import BaseDriver
+from qiskit.chemistry.drivers import FermionicDriver
 
 
 class MolecularGroundStateEnergy:
     """ Molecular ground state energy chemistry application """
 
     def __init__(self,
-                 driver: BaseDriver,
+                 driver: FermionicDriver,
                  solver: Optional[MinimumEigensolver] = None,
                  transformation: TransformationType = TransformationType.FULL,
                  qubit_mapping: QubitMappingType = QubitMappingType.PARITY,
@@ -69,12 +69,12 @@ def __init__(self,
         self._z2symmetry_reduction = z2symmetry_reduction
 
     @property
-    def driver(self) -> BaseDriver:
+    def driver(self) -> FermionicDriver:
         """ Returns chemistry driver """
         return self._driver
 
     @driver.setter
-    def driver(self, driver: BaseDriver) -> None:
+    def driver(self, driver: FermionicDriver) -> None:
         self._driver = driver
 
     @property

qiskit/chemistry/drivers/__init__.py

@@ -51,6 +51,7 @@
    :nosignatures:
 
    BaseDriver
+   FermionicDriver
 
 Driver Common
 =============
@@ -59,8 +60,9 @@
    :toctree: ../stubs/
    :nosignatures:
 
-   UnitsType
+   Molecule
    HFMethodType
+   UnitsType
    BasisType
    InitialGuess
 
@@ -111,17 +113,23 @@
 
 
 """
-from ._basedriver import BaseDriver, UnitsType, HFMethodType
+
+from .base_driver import BaseDriver
+from .molecule import Molecule
+from .fermionic_driver import FermionicDriver, HFMethodType
+from .units_type import UnitsType
 from .fcidumpd import FCIDumpDriver
 from .gaussiand import GaussianDriver, GaussianLogDriver, GaussianLogResult
 from .hdf5d import HDF5Driver
 from .psi4d import PSI4Driver
 from .pyquanted import PyQuanteDriver, BasisType
 from .pyscfd import PySCFDriver, InitialGuess
 
-__all__ = ['BaseDriver',
+__all__ = ['HFMethodType',
+           'Molecule',
+           'BaseDriver',
+           'FermionicDriver',
            'UnitsType',
-           'HFMethodType',
            'FCIDumpDriver',
            'GaussianDriver',
            'GaussianLogDriver',

qiskit/chemistry/drivers/base_driver.py

@@ -0,0 +1,93 @@
+# This code is part of Qiskit.
+#
+# (C) Copyright IBM 2018, 2020.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
+
+"""
+This module implements the abstract base class for driver modules.
+"""
+
+from typing import Optional
+from abc import ABC, abstractmethod
+
+from .molecule import Molecule
+from ..qiskit_chemistry_error import QiskitChemistryError
+
+
+class BaseDriver(ABC):
+    """
+    Base class for Qiskit's chemistry drivers.
+    """
+
+    @abstractmethod
+    def __init__(self,
+                 molecule: Optional[Molecule] = None,
+                 basis: str = 'sto3g',
+                 hf_method: str = 'rhf',
+                 supports_molecule: bool = False) -> None:
+        """
+        Args:
+            molecule: molecule
+            basis: basis set
+            hf_method: Hartree-Fock Method type
+            supports_molecule: Indicates if driver supports molecule
+
+        Raises:
+            QiskitChemistryError: Molecule passed but driver doesn't support it.
+        """
+        if molecule is not None and not supports_molecule:
+            raise QiskitChemistryError("Driver doesn't support molecule.")
+
+        self._molecule = molecule
+        self._basis = basis
+        self._hf_method = hf_method
+        self._supports_molecule = supports_molecule
+
+    @property
+    def supports_molecule(self) -> bool:
+        """
+        True for derived classes that support Molecule.
+
+        Returns:
+            True if Molecule is supported.
+        """
+        return self._supports_molecule
+
+    @property
+    def molecule(self) -> Optional[Molecule]:
+        """ return molecule """
+        return self._molecule
+
+    @molecule.setter
+    def molecule(self, value: Molecule) -> None:
+        """ set molecule """
+        if not self.supports_molecule:
+            raise QiskitChemistryError("Driver doesn't support molecule.")
+        self._molecule = value
+
+    @property
+    def basis(self) -> str:
+        """ return basis """
+        return self._basis
+
+    @basis.setter
+    def basis(self, value: str) -> None:
+        """ set basis """
+        self._basis = value
+
+    @property
+    def hf_method(self) -> str:
+        """ return Hartree-Fock method """
+        return self._hf_method
+
+    @hf_method.setter
+    def hf_method(self, value: str) -> None:
+        """ set Hartree-Fock method """
+        self._hf_method = value

qiskit/chemistry/drivers/fcidumpd/fcidumpdriver.py

@@ -13,8 +13,9 @@
 """FCIDump Driver."""
 
 from typing import List, Optional
-from qiskit.chemistry.drivers import BaseDriver
-from qiskit.chemistry import QiskitChemistryError, QMolecule
+from ..base_driver import BaseDriver
+from ...qiskit_chemistry_error import QiskitChemistryError
+from ...qmolecule import QMolecule
 from .dumper import dump
 from .parser import parse
 
@@ -70,7 +71,7 @@ def run(self) -> QMolecule:
         q_mol.nuclear_repulsion_energy = fcidump_data.get('ecore', None)
         q_mol.num_orbitals = fcidump_data.get('NORB')
         q_mol.multiplicity = fcidump_data.get('MS2', 0) + 1
-        q_mol.charge = 0  # ensures QMolecule.log() works
+        q_mol.molecular_charge = 0  # ensures QMolecule.log() works
         q_mol.num_beta = (fcidump_data.get('NELEC') - (q_mol.multiplicity - 1)) // 2
         q_mol.num_alpha = fcidump_data.get('NELEC') - q_mol.num_beta
         if self.atoms is not None:

qiskit/chemistry/drivers/_basedriver.py → qiskit/chemistry/drivers/fermionic_driver.py

@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2018, 2020.
+# (C) Copyright IBM 2020.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
@@ -11,19 +11,14 @@
 # that they have been altered from the originals.
 
 """
-This module implements the abstract base class for driver modules.
+This module implements the abstract base class for fermionic driver modules.
 """
 
-from abc import ABC, abstractmethod
+from abc import abstractmethod
 from enum import Enum
 
-from qiskit.chemistry import QMolecule
-
-
-class UnitsType(Enum):
-    """ Units Type Enum """
-    ANGSTROM = 'Angstrom'
-    BOHR = 'Bohr'
+from ..qmolecule import QMolecule
+from .base_driver import BaseDriver
 
 
 class HFMethodType(Enum):
@@ -33,15 +28,11 @@ class HFMethodType(Enum):
     UHF = 'uhf'
 
 
-class BaseDriver(ABC):
+class FermionicDriver(BaseDriver):
     """
-    Base class for Qiskit's chemistry drivers.
+    Base class for Qiskit's chemistry fermionic drivers.
     """
 
-    @abstractmethod
-    def __init__(self):
-        pass
-
     @abstractmethod
     def run(self) -> QMolecule:
         """

qiskit/chemistry/drivers/gaussiand/gaussian_log_driver.py

@@ -15,14 +15,15 @@
 from typing import Union, List
 import logging
 
-from qiskit.chemistry import QiskitChemistryError
+from ..base_driver import BaseDriver
+from ...qiskit_chemistry_error import QiskitChemistryError
 from .gaussian_utils import check_valid, run_g16
 from .gaussian_log_result import GaussianLogResult
 
 logger = logging.getLogger(__name__)
 
 
-class GaussianLogDriver:
+class GaussianLogDriver(BaseDriver):
     """  Gaussian™ 16 log driver.
 
     Qiskit chemistry driver using the Gaussian™ 16 program that provides the log
@@ -55,6 +56,7 @@ def __init__(self, jcf: Union[str, List[str]]) -> None:
             jcf = '\n'.join(jcf)
 
         self._jcf = jcf
+        super().__init__()
 
     @staticmethod
     def _check_valid():

qiskit/chemistry/drivers/gaussiand/gaussiandriver.py

@@ -12,21 +12,24 @@
 
 """ Gaussian Driver """
 
-from typing import Union, List
+from typing import Union, List, Optional
 import sys
 import io
 import logging
 import os
 import tempfile
 import numpy as np
-from qiskit.chemistry import QMolecule, QiskitChemistryError
-from qiskit.chemistry.drivers import BaseDriver
+from ..units_type import UnitsType
+from ..fermionic_driver import FermionicDriver
+from ...qiskit_chemistry_error import QiskitChemistryError
+from ..molecule import Molecule
+from ...qmolecule import QMolecule
 from .gaussian_utils import check_valid, run_g16
 
 logger = logging.getLogger(__name__)
 
 
-class GaussianDriver(BaseDriver):
+class GaussianDriver(FermionicDriver):
     """
     Qiskit chemistry driver using the Gaussian™ 16 program.
 
@@ -42,29 +45,64 @@ class GaussianDriver(BaseDriver):
     def __init__(self,
                  config: Union[str, List[str]] =
                  '# rhf/sto-3g scf(conventional)\n\n'
-                 'h2 molecule\n\n0 1\nH   0.0  0.0    0.0\nH   0.0  0.0    0.735\n\n') -> None:
+                 'h2 molecule\n\n0 1\nH   0.0  0.0    0.0\nH   0.0  0.0    0.735\n\n',
+                 molecule: Optional[Molecule] = None,
+                 basis: str = 'sto-3g',
+                 hf_method: str = 'rhf') -> None:
         """
         Args:
-            config: A molecular configuration conforming to Gaussian™ 16 format
+            config: A molecular configuration conforming to Gaussian™ 16 format.
+            molecule: A driver independent Molecule definition instance may be provided. When
+                a molecule is supplied the `config` parameter is ignored and the Molecule instance,
+                along with `basis` and `hf_method` is used to build a basic config instead.
+                The Molecule object is read when the driver is run and converted to the driver
+                dependent configuration for the computation. This allows, for example, the Molecule
+                geometry to be updated to compute different points.
+            basis: Basis set
+            hf_method: Hartree-Fock Method type; `rhf`, `rohf`, `uhf`
+
         Raises:
             QiskitChemistryError: Invalid Input
         """
         GaussianDriver._check_valid()
-        if not isinstance(config, list) and not isinstance(config, str):
-            raise QiskitChemistryError("Invalid input for Gaussian Driver '{}'".format(config))
+        if not isinstance(config, str) and not isinstance(config, list):
+            raise QiskitChemistryError("Invalid config for Gaussian Driver '{}'".format(config))
 
         if isinstance(config, list):
             config = '\n'.join(config)
 
-        super().__init__()
+        super().__init__(molecule=molecule,
+                         basis=basis,
+                         hf_method=hf_method,
+                         supports_molecule=True)
         self._config = config
 
     @staticmethod
     def _check_valid():
         check_valid()
 
+    def _from_molecule_to_str(self) -> str:
+        units = None
+        if self.molecule.units == UnitsType.ANGSTROM:
+            units = 'Angstrom'
+        elif self.molecule.units == UnitsType.BOHR:
+            units = 'Bohr'
+        else:
+            raise QiskitChemistryError("Unknown unit '{}'".format(self.molecule.units.value))
+        cfg1 = f'# {self.hf_method}/{self.basis} UNITS={units} scf(conventional)\n\n'
+        name = ''.join([name for (name, _) in self.molecule.geometry])
+        geom = '\n'.join([name + ' ' + ' '.join(map(str, coord))
+                          for (name, coord) in self.molecule.geometry])
+        cfg2 = f'{name} molecule\n\n'
+        cfg3 = f'{self.molecule.charge} {self.molecule.multiplicity}\n{geom}\n\n'
+        return cfg1 + cfg2 + cfg3
+
     def run(self) -> QMolecule:
-        cfg = self._config
+        if self.molecule is not None:
+            cfg = self._from_molecule_to_str()
+        else:
+            cfg = self._config
+
         while not cfg.endswith('\n\n'):
             cfg += '\n'
 
@@ -93,7 +131,7 @@ def run(self) -> QMolecule:
             logger.warning("Failed to remove MatrixElement file %s", fname)
 
         q_mol.origin_driver_name = 'GAUSSIAN'
-        q_mol.origin_driver_config = self._config
+        q_mol.origin_driver_config = cfg
         return q_mol
 
     @staticmethod