HDF5-Property framework integration

.pylintdict

@@ -166,6 +166,7 @@ hardcoded
 hartree
 hartrees
 hcore
+hdf
 heidelberg
 heisenberg
 hermite
@@ -192,6 +193,7 @@ intel
 intelvem
 interatomic
 internuclear
+interpretable
 ints
 ising
 iso
@@ -221,6 +223,7 @@ knowles
 kohn
 kwarg
 kwargs
+kwds
 labelled
 lda
 len

docs/apidocs/qiskit_nature.hdf5.rst

@@ -0,0 +1,17 @@
+HDF5
+==================
+
+.. _qiskit_nature-hdf5:
+
+.. automodule:: qiskit_nature.hdf5
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      load_from_hdf5
+      save_to_hdf5
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      HDF5Storable

docs/tutorials/08_property_framework.ipynb

@@ -708,11 +708,11 @@
       "\t\t\tAlpha\n",
       "\t\t\t<(2, 2) matrix with 2 non-zero entries>\n",
       "\t\t\t[0, 0] = -1.2563390730032498\n",
-      "\t\t\t[1, 1] = -0.4718960072811426\n",
+      "\t\t\t[1, 1] = -0.47189600728114245\n",
       "\t\t\tBeta\n",
       "\t\t\t<(2, 2) matrix with 2 non-zero entries>\n",
       "\t\t\t[0, 0] = -1.2563390730032498\n",
-      "\t\t\t[1, 1] = -0.4718960072811426\n",
+      "\t\t\t[1, 1] = -0.47189600728114245\n",
       "\t\t(MO) 2-Body Terms:\n",
       "\t\t\tAlpha-Alpha\n",
       "\t\t\t<(2, 2, 2, 2) matrix with 8 non-zero entries>\n",
@@ -785,15 +785,15 @@
       "\t\t\t\tAlpha\n",
       "\t\t\t\t<(2, 2) matrix with 4 non-zero entries>\n",
       "\t\t\t\t[0, 0] = 0.6944743507776598\n",
-      "\t\t\t\t[0, 1] = -0.9278334704592321\n",
+      "\t\t\t\t[0, 1] = -0.927833470459232\n",
       "\t\t\t\t[1, 0] = -0.9278334704592321\n",
-      "\t\t\t\t[1, 1] = 0.6944743507776601\n",
+      "\t\t\t\t[1, 1] = 0.6944743507776604\n",
       "\t\t\t\tBeta\n",
       "\t\t\t\t<(2, 2) matrix with 4 non-zero entries>\n",
       "\t\t\t\t[0, 0] = 0.6944743507776598\n",
-      "\t\t\t\t[0, 1] = -0.9278334704592321\n",
+      "\t\t\t\t[0, 1] = -0.927833470459232\n",
       "\t\t\t\t[1, 0] = -0.9278334704592321\n",
-      "\t\t\t\t[1, 1] = 0.6944743507776601\n",
+      "\t\t\t\t[1, 1] = 0.6944743507776604\n",
       "\tAngularMomentum:\n",
       "\t\t4 SOs\n",
       "\tMagnetization:\n",
@@ -1047,6 +1047,8 @@
     "from itertools import product\n",
     "from typing import List\n",
     "\n",
+    "import h5py\n",
+    "\n",
     "from qiskit_nature.drivers import QMolecule\n",
     "from qiskit_nature.operators.second_quantization import FermionicOp\n",
     "from qiskit_nature.properties.second_quantization.electronic.bases import ElectronicBasis\n",
@@ -1078,6 +1080,16 @@
     "        string += [f\"\\t{self._num_molecular_orbitals} MOs\"]\n",
     "        return \"\\n\".join(string)\n",
     "\n",
+    "    def to_hdf5(self, parent: h5py.Group) -> None:\n",
+    "        super().to_hdf5(parent)\n",
+    "        group = parent.require_group(self.name)\n",
+    "\n",
+    "        group.attrs[\"num_molecular_orbitals\"] = self._num_molecular_orbitals\n",
+    "\n",
+    "    @classmethod\n",
+    "    def from_hdf5(cls, h5py_group: h5py.Group) -> \"ElectronicDensity\":\n",
+    "        return ElectronicDensity(h5py_group.attrs[\"num_molecular_orbitals\"])\n",
+    "\n",
     "    @classmethod\n",
     "    def from_legacy_driver_result(cls, result) -> \"ElectronicDensity\":\n",
     "        cls._validate_input_type(result, QMolecule)\n",
@@ -1217,7 +1229,7 @@
     {
      "data": {
       "text/html": [
-       "<h3>Version Information</h3><table><tr><th>Qiskit Software</th><th>Version</th></tr><tr><td><code>qiskit-terra</code></td><td>0.20.0.dev0+7af16a3</td></tr><tr><td><code>qiskit-aer</code></td><td>0.10.2</td></tr><tr><td><code>qiskit-ignis</code></td><td>0.7.0</td></tr><tr><td><code>qiskit-nature</code></td><td>0.4.0</td></tr><tr><td><code>qiskit-finance</code></td><td>0.4.0</td></tr><tr><td><code>qiskit-optimization</code></td><td>0.4.0</td></tr><tr><td><code>qiskit-machine-learning</code></td><td>0.3.0</td></tr><tr><th>System information</th></tr><tr><td>Python version</td><td>3.8.12</td></tr><tr><td>Python compiler</td><td>Clang 10.0.0 </td></tr><tr><td>Python build</td><td>default, Oct 12 2021 06:23:56</td></tr><tr><td>OS</td><td>Darwin</td></tr><tr><td>CPUs</td><td>2</td></tr><tr><td>Memory (Gb)</td><td>12.0</td></tr><tr><td colspan='2'>Fri Feb 04 13:55:22 2022 EST</td></tr></table>"
+       "<h3>Version Information</h3><table><tr><th>Qiskit Software</th><th>Version</th></tr><tr><td><code>qiskit-terra</code></td><td>0.20.0.dev0+9a743fb</td></tr><tr><td><code>qiskit-aer</code></td><td>0.11.0</td></tr><tr><td><code>qiskit-ignis</code></td><td>0.7.0</td></tr><tr><td><code>qiskit-ibmq-provider</code></td><td>0.19.0.dev0+8455b01</td></tr><tr><td><code>qiskit-nature</code></td><td>0.4.0</td></tr><tr><th>System information</th></tr><tr><td>Python version</td><td>3.9.9</td></tr><tr><td>Python compiler</td><td>GCC 11.2.1 20210728 (Red Hat 11.2.1-1)</td></tr><tr><td>Python build</td><td>main, Nov 19 2021 00:00:00</td></tr><tr><td>OS</td><td>Linux</td></tr><tr><td>CPUs</td><td>4</td></tr><tr><td>Memory (Gb)</td><td>14.842281341552734</td></tr><tr><td colspan='2'>Mon Jan 24 14:34:24 2022 CET</td></tr></table>"
       ],
       "text/plain": [
        "<IPython.core.display.HTML object>"
@@ -1245,6 +1257,14 @@
     "%qiskit_version_table\n",
     "%qiskit_copyright"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "889fbac9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -1263,7 +1283,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.9"
   }
  },
  "nbformat": 4,

qiskit_nature/__init__.py

@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2018, 2021.
+# (C) Copyright IBM 2018, 2022.
 #
 # 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
@@ -39,6 +39,7 @@
    circuit
    converters
    drivers
+   hdf5
    mappers
    operators
    problems

qiskit_nature/drivers/molecule.py

@@ -17,6 +17,7 @@
 from typing import Callable, Tuple, List, Optional, cast
 import copy
 
+import h5py
 import numpy as np
 import scipy.linalg
 
@@ -36,6 +37,8 @@ class Molecule:
     directly if its needed.
     """
 
+    VERSION = 1
+
     def __init__(
         self,
         geometry: List[Tuple[str, List[float]]],
@@ -76,6 +79,71 @@ def __init__(
 
         self._perturbations = None  # type: Optional[List[float]]
 
+    def to_hdf5(self, parent: h5py.Group) -> None:
+        """Stores this instance in an HDF5 group inside of the provided parent group.
+
+        See also :func:`~qiskit_nature.hdf5.HDF5Storable.to_hdf5` for more details.
+
+        Args:
+            parent: the parent HDF5 group.
+        """
+        group = parent.require_group(self.__class__.__name__)
+        group.attrs["__class__"] = self.__class__.__name__
+        group.attrs["__module__"] = self.__class__.__module__
+        group.attrs["__version__"] = self.VERSION
+
+        geometry_group = group.create_group("geometry", track_order=True)
+        for idx, geom in enumerate(self._geometry):
+            symbol, coords = geom
+            geometry_group.create_dataset(str(idx), data=coords)
+            geometry_group[str(idx)].attrs["symbol"] = symbol
+
+        group.attrs["units"] = self.units.value
+        group.attrs["multiplicity"] = self.multiplicity
+        group.attrs["charge"] = self.charge
+
+        if self._masses:
+            group.create_dataset("masses", data=self._masses)
+
+    @staticmethod
+    def from_hdf5(h5py_group: h5py.Group) -> Molecule:
+        """Constructs a new instance from the data stored in the provided HDF5 group.
+
+        See also :func:`~qiskit_nature.hdf5.HDF5Storable.from_hdf5` for more details.
+
+        Args:
+            h5py_group: the HDF5 group from which to load the data.
+
+        Returns:
+            A new instance of this class.
+        """
+        geometry = []
+        for atom in h5py_group["geometry"].values():
+            geometry.append((atom.attrs["symbol"], list(atom[...])))
+
+        units: UnitsType
+        for unit in UnitsType:
+            if unit.value == h5py_group.attrs["units"]:
+                units = unit
+                break
+        else:
+            units = UnitsType.ANGSTROM
+
+        multiplicity = h5py_group.attrs["multiplicity"]
+        charge = h5py_group.attrs["charge"]
+
+        masses = None
+        if "masses" in h5py_group.keys():
+            masses = list(h5py_group["masses"])
+
+        return Molecule(
+            geometry,
+            multiplicity=multiplicity,
+            charge=charge,
+            units=units,
+            masses=masses,
+        )
+
     def __str__(self) -> str:
         string = ["Molecule:"]
         string += [f"\tMultiplicity: {self._multiplicity}"]

qiskit_nature/drivers/second_quantization/electronic_structure_driver.py

@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2020, 2021.
+# (C) Copyright IBM 2020, 2022.
 #
 # 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
@@ -17,7 +17,7 @@
 from abc import abstractmethod
 from enum import Enum
 
-from qiskit_nature.properties.second_quantization.electronic.types import GroupedElectronicProperty
+from qiskit_nature.properties.second_quantization.electronic import ElectronicStructureDriverResult
 from .base_driver import BaseDriver
 
 
@@ -43,6 +43,6 @@ class ElectronicStructureDriver(BaseDriver):
     """
 
     @abstractmethod
-    def run(self) -> GroupedElectronicProperty:
-        """Returns a GroupedElectronicProperty output as produced by the driver."""
+    def run(self) -> ElectronicStructureDriverResult:
+        """Returns a ElectronicStructureDriverResult output as produced by the driver."""
         pass

qiskit_nature/drivers/second_quantization/electronic_structure_molecule_driver.py

@@ -20,7 +20,7 @@
 from enum import Enum
 
 from qiskit.exceptions import MissingOptionalLibraryError
-from qiskit_nature.properties.second_quantization.electronic.types import GroupedElectronicProperty
+from qiskit_nature.properties.second_quantization.electronic import ElectronicStructureDriverResult
 from .electronic_structure_driver import ElectronicStructureDriver, MethodType
 from ..molecule import Molecule
 from ...exceptions import UnsupportMethodError
@@ -169,7 +169,7 @@ def driver_kwargs(self, value: Optional[Dict[str, Any]]) -> None:
         """set driver kwargs"""
         self._driver_kwargs = value
 
-    def run(self) -> GroupedElectronicProperty:
+    def run(self) -> ElectronicStructureDriverResult:
         driver_class = ElectronicStructureDriverType.driver_class_from_type(
             self.driver_type, self.method
         )

qiskit_nature/drivers/second_quantization/pyquanted/pyquantedriver.py

@@ -24,7 +24,6 @@
 
 from qiskit_nature import QiskitNatureError
 from qiskit_nature.constants import BOHR, PERIODIC_TABLE
-from qiskit_nature.settings import settings
 from qiskit_nature.properties.second_quantization.driver_metadata import DriverMetadata
 from qiskit_nature.properties.second_quantization.electronic import (
     ElectronicStructureDriverResult,
@@ -406,9 +405,11 @@ def _construct_driver_result(self) -> ElectronicStructureDriverResult:
         self._populate_driver_result_particle_number(driver_result)
         self._populate_driver_result_electronic_energy(driver_result)
 
-        if not settings.dict_aux_operators:
-            driver_result.add_property(AngularMomentum(self._nmo * 2))
-            driver_result.add_property(Magnetization(self._nmo * 2))
+        # TODO: once https://github.com/Qiskit/qiskit-nature/issues/312 is fixed we can stop adding
+        # these properties by default.
+        # if not settings.dict_aux_operators:
+        driver_result.add_property(AngularMomentum(self._nmo * 2))
+        driver_result.add_property(Magnetization(self._nmo * 2))
 
         return driver_result
 

qiskit_nature/drivers/second_quantization/pyscfd/pyscfdriver.py

@@ -22,6 +22,7 @@
 
 import numpy as np
 from qiskit.utils.validation import validate_min
+
 from qiskit_nature.properties.second_quantization.driver_metadata import DriverMetadata
 from qiskit_nature.properties.second_quantization.electronic import (
     ElectronicStructureDriverResult,
@@ -516,9 +517,9 @@ def _construct_driver_result(self) -> ElectronicStructureDriverResult:
         self._populate_driver_result_electronic_energy(driver_result)
         self._populate_driver_result_electronic_dipole_moment(driver_result)
 
-        # TODO: once https://github.com/Qiskit/qiskit-terra/issues/6772 is resolved, we no longer
-        # _have_ to add these properties. However, until then the interpret method relies on indices
-        # of the aux_operators which are incorrect if these properties are not added.
+        # TODO: once https://github.com/Qiskit/qiskit-nature/issues/312 is fixed we can stop adding
+        # these properties by default.
+        # if not settings.dict_aux_operators:
         driver_result.add_property(AngularMomentum(self._mol.nao * 2))
         driver_result.add_property(Magnetization(self._mol.nao * 2))
 

qiskit_nature/drivers/second_quantization/vibrational_structure_driver.py

@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2020, 2021.
+# (C) Copyright IBM 2020, 2022.
 #
 # 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
@@ -16,8 +16,8 @@
 
 from abc import abstractmethod
 
-from qiskit_nature.properties.second_quantization.vibrational.types import (
-    GroupedVibrationalProperty,
+from qiskit_nature.properties.second_quantization.vibrational import (
+    VibrationalStructureDriverResult,
 )
 from .base_driver import BaseDriver
 
@@ -28,6 +28,6 @@ class VibrationalStructureDriver(BaseDriver):
     """
 
     @abstractmethod
-    def run(self) -> GroupedVibrationalProperty:
-        """Returns a GroupedVibrationalProperty output as produced by the driver."""
+    def run(self) -> VibrationalStructureDriverResult:
+        """Returns a VibrationalStructureDriverResult output as produced by the driver."""
         pass

qiskit_nature/drivers/second_quantization/vibrational_structure_molecule_driver.py

@@ -20,8 +20,8 @@
 from enum import Enum
 
 from qiskit.exceptions import MissingOptionalLibraryError
-from qiskit_nature.properties.second_quantization.vibrational.types import (
-    GroupedVibrationalProperty,
+from qiskit_nature.properties.second_quantization.vibrational import (
+    VibrationalStructureDriverResult,
 )
 from .vibrational_structure_driver import VibrationalStructureDriver
 from ..molecule import Molecule
@@ -146,7 +146,7 @@ def driver_kwargs(self, value: Optional[Dict[str, Any]]) -> None:
         """set driver kwargs"""
         self._driver_kwargs = value
 
-    def run(self) -> GroupedVibrationalProperty:
+    def run(self) -> VibrationalStructureDriverResult:
         driver_class = VibrationalStructureDriverType.driver_class_from_type(self.driver_type)
         driver = driver_class.from_molecule(  # type: ignore
             self.molecule, self.basis, self.driver_kwargs