Refactor Chemistry Drivers

qiskit/chemistry/__init__.py

@@ -137,6 +137,7 @@
 
    BosonicOperator
    FermionicOperator
+   Molecule
    QMolecule
    MP2Info
 
@@ -155,6 +156,7 @@
 """
 
 from .qiskit_chemistry_error import QiskitChemistryError
+from .molecule import Molecule
 from .qmolecule import QMolecule
 from .bosonic_operator import BosonicOperator
 from .fermionic_operator import FermionicOperator
@@ -163,6 +165,7 @@
                        set_qiskit_chemistry_logging)
 
 __all__ = ['QiskitChemistryError',
+           'Molecule',
            'QMolecule',
            'BosonicOperator',
            'FermionicOperator',

qiskit/chemistry/applications/molecular_ground_state_energy.py

@@ -23,14 +23,14 @@
 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 IntegralsDriver
 
 
 class MolecularGroundStateEnergy:
     """ Molecular ground state energy chemistry application """
 
     def __init__(self,
-                 driver: BaseDriver,
+                 driver: IntegralsDriver,
                  solver: Optional[MinimumEigensolver] = None,
                  transformation: TransformationType = TransformationType.FULL,
                  qubit_mapping: QubitMappingType = QubitMappingType.PARITY,
@@ -68,12 +68,12 @@ def __init__(self,
         self._z2symmetry_reduction = z2symmetry_reduction
 
     @property
-    def driver(self) -> BaseDriver:
+    def driver(self) -> IntegralsDriver:
         """ Returns chemistry driver """
         return self._driver
 
     @driver.setter
-    def driver(self, driver: BaseDriver) -> None:
+    def driver(self, driver: IntegralsDriver) -> None:
         self._driver = driver
 
     @property

qiskit/chemistry/drivers/__init__.py

@@ -51,6 +51,7 @@
    :nosignatures:
 
    BaseDriver
+   IntegralsDriver
 
 Driver Common
 =============
@@ -59,8 +60,8 @@
    :toctree: ../stubs/
    :nosignatures:
 
-   UnitsType
    HFMethodType
+   UnitsType
    BasisType
    InitialGuess
 
@@ -111,17 +112,20 @@
 
 
 """
-from ._basedriver import BaseDriver, UnitsType, HFMethodType
+
+from .base_driver import BaseDriver
+from .integrals_driver import IntegralsDriver, UnitsType, HFMethodType
 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',
+           'BaseDriver',
+           'IntegralsDriver',
            'UnitsType',
-           'HFMethodType',
            'FCIDumpDriver',
            'GaussianDriver',
            'GaussianLogDriver',

qiskit/chemistry/drivers/base_driver.py

@@ -0,0 +1,23 @@
+# 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 abc import ABC
+
+
+class BaseDriver(ABC):
+    """
+    Base class for Qiskit's chemistry drivers.
+    """

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/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

qiskit/chemistry/drivers/gaussiand/gaussiandriver.py

@@ -19,14 +19,16 @@
 import os
 import tempfile
 import numpy as np
-from qiskit.chemistry import QMolecule, QiskitChemistryError
-from qiskit.chemistry.drivers import BaseDriver
+from ..integrals_driver import IntegralsDriver
+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(IntegralsDriver):
     """
     Qiskit chemistry driver using the Gaussian™ 16 program.
 
@@ -40,17 +42,20 @@ class GaussianDriver(BaseDriver):
     """
 
     def __init__(self,
-                 config: Union[str, List[str]] =
+                 config: Union[str, List[str], Molecule] =
                  '# 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:
         """
         Args:
-            config: A molecular configuration conforming to Gaussian™ 16 format
+            config: A molecular configuration conforming to Gaussian™ 16 format or
+                    a molecule object
         Raises:
             QiskitChemistryError: Invalid Input
         """
         GaussianDriver._check_valid()
-        if not isinstance(config, list) and not isinstance(config, str):
+        if not isinstance(config, str) and \
+                not isinstance(config, list) and \
+                not isinstance(config, Molecule):
             raise QiskitChemistryError("Invalid input for Gaussian Driver '{}'".format(config))
 
         if isinstance(config, list):
@@ -63,8 +68,23 @@ def __init__(self,
     def _check_valid():
         check_valid()
 
+    @staticmethod
+    def _from_molecule_to_str(mol: Molecule) -> str:
+        cfg1 = '# {}/{} scf(conventional)\n\n'.format(
+            mol.hf_method, mol.basis_set)
+        name = ''.join([name for (name, _) in mol.geometry])
+        geom = '\n'.join([name + ' ' + ' '.join(map(str, coord))
+                          for (name, coord) in mol.geometry])
+        cfg2 = '{} molecule\n\n{} {}\n{}\n\n'.format(
+            name, mol.charge, mol.multiplicity, geom)
+        return cfg1 + cfg2
+
     def run(self) -> QMolecule:
-        cfg = self._config
+        if isinstance(self._config, Molecule):
+            cfg = GaussianDriver._from_molecule_to_str(self._config)
+        else:
+            cfg = self._config
+
         while not cfg.endswith('\n\n'):
             cfg += '\n'
 
@@ -93,7 +113,7 @@ 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

qiskit/chemistry/drivers/hdf5d/hdf5driver.py

@@ -14,8 +14,8 @@
 
 import os
 import logging
-from qiskit.chemistry.drivers import BaseDriver
-from qiskit.chemistry import QMolecule
+from ..base_driver import BaseDriver
+from ...qmolecule import QMolecule
 
 logger = logging.getLogger(__name__)
 
@@ -48,6 +48,15 @@ def work_path(self, new_work_path):
         self._work_path = new_work_path
 
     def run(self) -> QMolecule:
+        """
+        Runs driver to produce a QMolecule output.
+
+        Returns:
+            A QMolecule containing the molecular data.
+
+        Raises:
+            LookupError: file not found.
+        """
         hdf5_file = self._hdf5_input
         if self.work_path is not None and not os.path.isabs(hdf5_file):
             hdf5_file = os.path.abspath(os.path.join(self.work_path, hdf5_file))

qiskit/chemistry/drivers/_basedriver.py → qiskit/chemistry/drivers/integrals_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
@@ -11,13 +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 integral driver modules.
 """
 
-from abc import ABC, abstractmethod
+from abc import abstractmethod
 from enum import Enum
 
-from qiskit.chemistry import QMolecule
+from ..qmolecule import QMolecule
+from .base_driver import BaseDriver
 
 
 class UnitsType(Enum):
@@ -33,15 +34,11 @@ class HFMethodType(Enum):
     UHF = 'uhf'
 
 
-class BaseDriver(ABC):
+class IntegralsDriver(BaseDriver):
     """
-    Base class for Qiskit's chemistry drivers.
+    Base class for Qiskit's chemistry integral drivers.
     """
 
-    @abstractmethod
-    def __init__(self):
-        pass
-
     @abstractmethod
     def run(self) -> QMolecule:
         """

qiskit/chemistry/drivers/psi4d/psi4driver.py

@@ -19,8 +19,10 @@
 import logging
 import sys
 from shutil import which
-from qiskit.chemistry import QMolecule, QiskitChemistryError
-from qiskit.chemistry.drivers import BaseDriver
+from ..integrals_driver import IntegralsDriver
+from ...qiskit_chemistry_error import QiskitChemistryError
+from ...molecule import Molecule
+from ...qmolecule import QMolecule
 
 logger = logging.getLogger(__name__)
 
@@ -29,25 +31,28 @@
 PSI4_APP = which(PSI4)
 
 
-class PSI4Driver(BaseDriver):
+class PSI4Driver(IntegralsDriver):
     """
     Qiskit chemistry driver using the PSI4 program.
 
     See http://www.psicode.org/
     """
 
     def __init__(self,
-                 config: Union[str, List[str]] =
+                 config: Union[str, List[str], Molecule] =
                  'molecule h2 {\n  0 1\n  H  0.0 0.0 0.0\n  H  0.0 0.0 0.735\n}\n\n'
                  'set {\n  basis sto-3g\n  scf_type pk\n  reference rhf\n') -> None:
         """
         Args:
-            config: A molecular configuration conforming to PSI4 format
+            config: A molecular configuration conforming to PSI4 format or
+                    a molecule object
         Raises:
             QiskitChemistryError: Invalid Input
         """
         self._check_valid()
-        if not isinstance(config, list) and not isinstance(config, str):
+        if not isinstance(config, str) and \
+                not isinstance(config, list) and \
+                not isinstance(config, Molecule):
             raise QiskitChemistryError("Invalid input for PSI4 Driver '{}'".format(config))
 
         if isinstance(config, list):
@@ -61,14 +66,30 @@ def _check_valid():
         if PSI4_APP is None:
             raise QiskitChemistryError("Could not locate {}".format(PSI4))
 
+    @staticmethod
+    def _from_molecule_to_str(mol: Molecule) -> str:
+        name = ''.join([name for (name, _) in mol.geometry])
+        geom = '\n'.join([name + ' ' + ' '.join(map(str, coord))
+                          for (name, coord) in mol.geometry])
+        cfg1 = 'molecule {} {{\n {} {}\n {}\nno_com\nno_reorient\n}}\n\n'.format(
+            name, mol.charge, mol.multiplicity, geom)
+        cfg2 = 'set {{\n basis {}\n scf_type pk\n reference {}\n}}'.format(
+            mol.basis_set, mol.hf_method)
+        return cfg1 + cfg2
+
     def run(self) -> QMolecule:
+        if isinstance(self._config, Molecule):
+            cfg = PSI4Driver._from_molecule_to_str(self._config)
+        else:
+            cfg = self._config
+
         psi4d_directory = os.path.dirname(os.path.realpath(__file__))
         template_file = psi4d_directory + '/_template.txt'
         qiskit_chemistry_directory = os.path.abspath(os.path.join(psi4d_directory, '../..'))
 
         molecule = QMolecule()
 
-        input_text = self._config + '\n'
+        input_text = cfg + '\n'
         input_text += 'import sys\n'
         syspath = '[\'' + qiskit_chemistry_directory + '\',\'' + '\',\''.join(sys.path) + '\']'
 
@@ -116,7 +137,7 @@ def run(self) -> QMolecule:
         # remove internal file
         _q_molecule.remove_file()
         _q_molecule.origin_driver_name = 'PSI4'
-        _q_molecule.origin_driver_config = self._config
+        _q_molecule.origin_driver_config = cfg
         return _q_molecule
 
     @staticmethod