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

@@ -129,16 +129,7 @@
    "execution_count": 3,
    "id": "11c080c5",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/oss/Files/Qiskit/.direnv/python-3.9.6/lib/python3.9/site-packages/pyscf/lib/misc.py:46: H5pyDeprecationWarning: Using default_file_mode other than 'r' is deprecated. Pass the mode to h5py.File() instead.\n",
-      "  h5py.get_config().default_file_mode = 'a'\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from qiskit_nature.properties.second_quantization.electronic import (\n",
     "    ElectronicEnergy,\n",
@@ -507,8 +498,8 @@
      "text": [
       "=== GROUND STATE ENERGY ===\n",
       " \n",
-      "* Electronic ground state energy (Hartree): -1\n",
-      "  - computed part:      -1\n"
+      "* Electronic ground state energy (Hartree): -1.\n",
+      "  - computed part:      -1.\n"
      ]
     }
    ],
@@ -634,7 +625,7 @@
       "ElectronicStructureDriverResult:\n",
       "\tDriverMetadata:\n",
       "\t\tProgram: PYSCF\n",
-      "\t\tVersion: 1.7.6\n",
+      "\t\tVersion: 2.0.1\n",
       "\t\tConfig:\n",
       "\t\t\tatom=H 0 0 0; H 0 0 0.735\n",
       "\t\t\tunit=Angstrom\n",
@@ -651,15 +642,15 @@
       "\t\tInitial basis: atomic\n",
       "\t\tFinal basis: molecular\n",
       "\t\tAlpha coefficients:\n",
-      "\t\t[0, 0] = 0.5483020229014736\n",
-      "\t\t[0, 1] = -1.2183273138546826\n",
+      "\t\t[0, 0] = 0.5483020229014732\n",
+      "\t\t[0, 1] = 1.2183273138546826\n",
       "\t\t[1, 0] = 0.548302022901473\n",
-      "\t\t[1, 1] = 1.2183273138546828\n",
+      "\t\t[1, 1] = -1.2183273138546826\n",
       "\t\tBeta coefficients:\n",
-      "\t\t[0, 0] = 0.5483020229014736\n",
-      "\t\t[0, 1] = -1.2183273138546826\n",
+      "\t\t[0, 0] = 0.5483020229014732\n",
+      "\t\t[0, 1] = 1.2183273138546826\n",
       "\t\t[1, 0] = 0.548302022901473\n",
-      "\t\t[1, 1] = 1.2183273138546828\n",
+      "\t\t[1, 1] = -1.2183273138546826\n",
       "\tParticleNumber:\n",
       "\t\t4 SOs\n",
       "\t\t1 alpha electrons\n",
@@ -671,15 +662,15 @@
       "\t\t\tAlpha\n",
       "\t\t\t<(2, 2) matrix with 4 non-zero entries>\n",
       "\t\t\t[0, 0] = -1.1242175791954514\n",
-      "\t\t\t[0, 1] = -0.9652573993472758\n",
-      "\t\t\t[1, 0] = -0.9652573993472758\n",
-      "\t\t\t[1, 1] = -1.1242175791954512\n",
+      "\t\t\t[0, 1] = -0.9652573993472754\n",
+      "\t\t\t[1, 0] = -0.9652573993472754\n",
+      "\t\t\t[1, 1] = -1.1242175791954514\n",
       "\t\t\tBeta\n",
       "\t\t\t<(2, 2) matrix with 4 non-zero entries>\n",
       "\t\t\t[0, 0] = -1.1242175791954514\n",
-      "\t\t\t[0, 1] = -0.9652573993472758\n",
-      "\t\t\t[1, 0] = -0.9652573993472758\n",
-      "\t\t\t[1, 1] = -1.1242175791954512\n",
+      "\t\t\t[0, 1] = -0.9652573993472754\n",
+      "\t\t\t[1, 0] = -0.9652573993472754\n",
+      "\t\t\t[1, 1] = -1.1242175791954514\n",
       "\t\t(AO) 2-Body Terms:\n",
       "\t\t\tAlpha-Alpha\n",
       "\t\t\t<(2, 2, 2, 2) matrix with 16 non-zero entries>\n",
@@ -716,44 +707,44 @@
       "\t\t(MO) 1-Body Terms:\n",
       "\t\t\tAlpha\n",
       "\t\t\t<(2, 2) matrix with 2 non-zero entries>\n",
-      "\t\t\t[0, 0] = -1.2563390730032507\n",
-      "\t\t\t[1, 1] = -0.47189600728114073\n",
+      "\t\t\t[0, 0] = -1.2563390730032498\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] = -1.2563390730032507\n",
-      "\t\t\t[1, 1] = -0.47189600728114073\n",
+      "\t\t\t[0, 0] = -1.2563390730032498\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",
-      "\t\t\t[0, 0, 0, 0] = 0.675710154803517\n",
-      "\t\t\t[0, 0, 1, 1] = 0.6645817302552974\n",
-      "\t\t\t[0, 1, 0, 1] = 0.18093119978423153\n",
-      "\t\t\t[0, 1, 1, 0] = 0.18093119978423136\n",
-      "\t\t\t[1, 0, 0, 1] = 0.18093119978423164\n",
+      "\t\t\t[0, 0, 0, 0] = 0.6757101548035161\n",
+      "\t\t\t[0, 0, 1, 1] = 0.6645817302552968\n",
+      "\t\t\t[0, 1, 0, 1] = 0.18093119978423136\n",
+      "\t\t\t[0, 1, 1, 0] = 0.18093119978423106\n",
+      "\t\t\t[1, 0, 0, 1] = 0.18093119978423144\n",
       "\t\t\t... skipping 3 entries\n",
       "\t\t\tBeta-Alpha\n",
       "\t\t\t<(2, 2, 2, 2) matrix with 8 non-zero entries>\n",
-      "\t\t\t[0, 0, 0, 0] = 0.675710154803517\n",
-      "\t\t\t[0, 0, 1, 1] = 0.6645817302552974\n",
-      "\t\t\t[0, 1, 0, 1] = 0.18093119978423153\n",
-      "\t\t\t[0, 1, 1, 0] = 0.18093119978423136\n",
-      "\t\t\t[1, 0, 0, 1] = 0.18093119978423164\n",
+      "\t\t\t[0, 0, 0, 0] = 0.6757101548035161\n",
+      "\t\t\t[0, 0, 1, 1] = 0.6645817302552968\n",
+      "\t\t\t[0, 1, 0, 1] = 0.18093119978423136\n",
+      "\t\t\t[0, 1, 1, 0] = 0.18093119978423106\n",
+      "\t\t\t[1, 0, 0, 1] = 0.18093119978423144\n",
       "\t\t\t... skipping 3 entries\n",
       "\t\t\tBeta-Beta\n",
       "\t\t\t<(2, 2, 2, 2) matrix with 8 non-zero entries>\n",
-      "\t\t\t[0, 0, 0, 0] = 0.675710154803517\n",
-      "\t\t\t[0, 0, 1, 1] = 0.6645817302552974\n",
-      "\t\t\t[0, 1, 0, 1] = 0.18093119978423153\n",
-      "\t\t\t[0, 1, 1, 0] = 0.18093119978423136\n",
-      "\t\t\t[1, 0, 0, 1] = 0.18093119978423164\n",
+      "\t\t\t[0, 0, 0, 0] = 0.6757101548035161\n",
+      "\t\t\t[0, 0, 1, 1] = 0.6645817302552968\n",
+      "\t\t\t[0, 1, 0, 1] = 0.18093119978423136\n",
+      "\t\t\t[0, 1, 1, 0] = 0.18093119978423106\n",
+      "\t\t\t[1, 0, 0, 1] = 0.18093119978423144\n",
       "\t\t\t... skipping 3 entries\n",
       "\t\t\tAlpha-Beta\n",
       "\t\t\t<(2, 2, 2, 2) matrix with 8 non-zero entries>\n",
-      "\t\t\t[0, 0, 0, 0] = 0.675710154803517\n",
-      "\t\t\t[0, 0, 1, 1] = 0.6645817302552974\n",
-      "\t\t\t[0, 1, 0, 1] = 0.18093119978423153\n",
-      "\t\t\t[0, 1, 1, 0] = 0.18093119978423136\n",
-      "\t\t\t[1, 0, 0, 1] = 0.18093119978423164\n",
+      "\t\t\t[0, 0, 0, 0] = 0.6757101548035161\n",
+      "\t\t\t[0, 0, 1, 1] = 0.6645817302552968\n",
+      "\t\t\t[0, 1, 0, 1] = 0.18093119978423136\n",
+      "\t\t\t[0, 1, 1, 0] = 0.18093119978423106\n",
+      "\t\t\t[1, 0, 0, 1] = 0.18093119978423144\n",
       "\t\t\t... skipping 3 entries\n",
       "\tElectronicDipoleMoment:\n",
       "\t\tDipoleMomentX\n",
@@ -782,27 +773,27 @@
       "\t\t\t(AO) 1-Body Terms:\n",
       "\t\t\t\tAlpha\n",
       "\t\t\t\t<(2, 2) matrix with 3 non-zero entries>\n",
-      "\t\t\t\t[0, 1] = 0.4605377079660319\n",
-      "\t\t\t\t[1, 0] = 0.4605377079660319\n",
-      "\t\t\t\t[1, 1] = 1.3889487015553204\n",
+      "\t\t\t\t[0, 1] = 0.46053770796603194\n",
+      "\t\t\t\t[1, 0] = 0.46053770796603194\n",
+      "\t\t\t\t[1, 1] = 1.3889487015553206\n",
       "\t\t\t\tBeta\n",
       "\t\t\t\t<(2, 2) matrix with 3 non-zero entries>\n",
-      "\t\t\t\t[0, 1] = 0.4605377079660319\n",
-      "\t\t\t\t[1, 0] = 0.4605377079660319\n",
-      "\t\t\t\t[1, 1] = 1.3889487015553204\n",
+      "\t\t\t\t[0, 1] = 0.46053770796603194\n",
+      "\t\t\t\t[1, 0] = 0.46053770796603194\n",
+      "\t\t\t\t[1, 1] = 1.3889487015553206\n",
       "\t\t\t(MO) 1-Body Terms:\n",
       "\t\t\t\tAlpha\n",
       "\t\t\t\t<(2, 2) matrix with 4 non-zero entries>\n",
-      "\t\t\t\t[0, 0] = 0.69447435077766\n",
-      "\t\t\t\t[0, 1] = 0.9278334704592323\n",
-      "\t\t\t\t[1, 0] = 0.9278334704592324\n",
-      "\t\t\t\t[1, 1] = 0.6944743507776605\n",
+      "\t\t\t\t[0, 0] = 0.6944743507776598\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] = 0.6944743507776604\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] = 0.69447435077766\n",
-      "\t\t\t\t[0, 1] = 0.9278334704592323\n",
-      "\t\t\t\t[1, 0] = 0.9278334704592324\n",
-      "\t\t\t\t[1, 1] = 0.6944743507776605\n",
+      "\t\t\t\t[0, 0] = 0.6944743507776598\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] = 0.6944743507776604\n",
       "\tAngularMomentum:\n",
       "\t\t4 SOs\n",
       "\tMagnetization:\n",
@@ -812,7 +803,7 @@
       "\tCharge: 0\n",
       "\tGeometry:\n",
       "\t\tH\t[0.0, 0.0, 0.0]\n",
-      "\t\tH\t[0.0, 0.0, 1.3889487015553204]\n",
+      "\t\tH\t[0.0, 0.0, 0.735]\n",
       "\tMasses:\n",
       "\t\tH\t1\n",
       "\t\tH\t1\n"
@@ -1061,6 +1052,8 @@
     "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",
@@ -1092,6 +1085,16 @@
     "        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",
@@ -1231,8 +1234,7 @@
     {
      "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>0.19.0.dev0+be0ed5f</td></tr><tr><td><code>qiskit-aer</code></td><td>0.9.0</td></tr><tr><td><code>qiskit-ignis</code></td><td>0.7.0.dev0+9201ed8</td></tr><tr><td><code>qiskit-ibmq-provider</code></td><td>0.16.0.dev0+4f6b7f6</td></tr><tr><td><code>qiskit-aqua</code></td><td>0.9.0.dev0+81239d0</td></tr><tr><td><code>qiskit-nature</code></td><td>0.2.0</td></tr><tr><th>System information</th></tr><tr><td>Python</td><td>3.9.6 (default, Jul 16 2021, 00:00:00) \n",
-       "[GCC 10.3.1 20210422 (Red Hat 10.3.1-1)]</td></tr><tr><td>OS</td><td>Linux</td></tr><tr><td>CPUs</td><td>4</td></tr><tr><td>Memory (Gb)</td><td>14.842548370361328</td></tr><tr><td colspan='2'>Wed Aug 18 09:35:15 2021 CEST</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>"
@@ -1244,7 +1246,7 @@
     {
      "data": {
       "text/html": [
-       "<div style='width: 100%; background-color:#d5d9e0;padding-left: 10px; padding-bottom: 10px; padding-right: 10px; padding-top: 5px'><h3>This code is a part of Qiskit</h3><p>&copy; Copyright IBM 2017, 2021.</p><p>This code is licensed under the Apache License, Version 2.0. You may<br>obtain a copy of this license in the LICENSE.txt file in the root directory<br> of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.<p>Any modifications or derivative works of this code must retain this<br>copyright notice, and modified files need to carry a notice indicating<br>that they have been altered from the originals.</p></div>"
+       "<div style='width: 100%; background-color:#d5d9e0;padding-left: 10px; padding-bottom: 10px; padding-right: 10px; padding-top: 5px'><h3>This code is a part of Qiskit</h3><p>&copy; Copyright IBM 2017, 2022.</p><p>This code is licensed under the Apache License, Version 2.0. You may<br>obtain a copy of this license in the LICENSE.txt file in the root directory<br> of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.<p>Any modifications or derivative works of this code must retain this<br>copyright notice, and modified files need to carry a notice indicating<br>that they have been altered from the originals.</p></div>"
       ],
       "text/plain": [
        "<IPython.core.display.HTML object>"
@@ -1260,6 +1262,14 @@
     "%qiskit_version_table\n",
     "%qiskit_copyright"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "889fbac9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -1278,7 +1288,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "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