Towards a non-driver future (qiskit-community#796)

* WIP: problem refactoring This is a first step towards decoupling the BaseProblem and BaseDriver interfaces. Instead of injecting drivers and transformers into a problem, these become the output of our driver classes. In turn, transformers now take entire problem instances as input and return them as output. This is an intermediate step towards the final form of the problem classes and this commit is not working fully. * refactor: make BaseProblem class instantiable * refactor: integrate PropertiesContainer * refactor: populate second_q.hamiltonians This moves the "main operators" into the new hamiltonians module and creates a base interface for these classes to follow. * refactor: extract lattice constructor methods to Lattice * refactor: remove unneeded Property subclasses * fix: some linting * fix: html generation * fix: add missing hamiltonian.interpret call * WIP: migrate driver to QCSchema * refactor: molecule dataclass - extracts a simple MoleculeInfo dataclass out of the original Molecule - moves UnitsType to DistanceType in the new units module (generalizing the concept of enumerating units) * fix: spelling * fix: PySCFDriver * fix HDF5Driver-based tests * fix: GaussianDriver * fix linters * refactor transformer tests * fix: handle optionals in unittests * fix: GaussianDriver.from_matrix_file * fix: README example * fix: tutorials * fix: slow PySCF-dependent test * fix: revert minor change to PySCFDriver * test: fix InitialPoint unittests * docs: replace open TODOs in docstrings * add reno * refactor: use direct type hints for Hamiltonians * fix: default to ANGSTROM unit in MoleculeInfo * fix: do not copy LatticeModel.lattice * fix: generalize MoleculeInfo.coords type * fix: remove unused loggers * refactor: enforce keyword arguments in drivers * refactor: extract _QCSchemaData * refactor: some QCSchema methods * fix: update some docstrings Co-authored-by: Steve Wood <[email protected]> * refactor: update argument name in transformers * refactor: extract np.asarray into reshape utility Co-authored-by: Steve Wood <[email protected]>
Anthony-Gandon · Sep 1, 2022 · 545d06c · 545d06c
1 parent b39d013
commit 545d06c
Show file tree

Hide file tree

Showing 175 changed files with 5,996 additions and 9,131 deletions.
diff --git a/.pylintdict b/.pylintdict
@@ -28,6 +28,7 @@ args
 arrowheads
 arrowstyle
 arxiv
+asarray
 asdict
 asparagine
 aspartic
@@ -121,6 +122,7 @@ dimens
 dimensionality
 dirac
 discoverable
+distanceunit
 distinguishability
 dll
 docstring
@@ -429,6 +431,7 @@ realise
 rebranding
 refactor
 refactored
+refactoring
 regs
 reinstall
 repr

diff --git a/README.md b/README.md
@@ -69,7 +69,7 @@ the ground-state (minimum) energy of a molecule.
 
 ```python
 from qiskit_nature.settings import settings
-from qiskit_nature.second_q.drivers import UnitsType
+from qiskit_nature.units import DistanceUnit
 from qiskit_nature.second_q.drivers import PySCFDriver
 from qiskit_nature.second_q.problems import ElectronicStructureProblem
 
@@ -79,14 +79,14 @@ settings.dict_aux_operators = True
 # package, to compute the one-body and two-body integrals in
 # electronic-orbital basis, necessary to form the Fermionic operator
 driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
-                     unit=UnitsType.ANGSTROM,
+                     unit=DistanceUnit.ANGSTROM,
                      basis='sto3g')
-problem = ElectronicStructureProblem(driver)
+problem = driver.run()
 
 # generate the second-quantized operators
 main_op, _ = problem.second_q_ops()
 
-particle_number = problem.grouped_property_transformed.get_property("ParticleNumber")
+particle_number = problem.properties.particle_number
 
 num_particles = (particle_number.num_alpha, particle_number.num_beta)
 num_spin_orbitals = particle_number.num_spin_orbitals

diff --git a/docs/apidocs/qiskit_nature.second_q.hamiltonians.lattices.rst b/docs/apidocs/qiskit_nature.second_q.hamiltonians.lattices.rst
@@ -0,0 +1,19 @@
+
+
+lattices
+=================================
+
+.. automodule:: qiskit_nature.second_q.hamiltonians.lattices
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/tutorials/01_electronic_structure.ipynb b/docs/tutorials/01_electronic_structure.ipynb
@@ -90,35 +90,17 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Couldn't find cython becke routine\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/manoel/opt/anaconda3/envs/Qiskitenv/lib/python3.8/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.second_q.drivers import UnitsType, Molecule\n",
-    "from qiskit_nature.second_q.drivers import (\n",
-    "    ElectronicStructureDriverType,\n",
-    "    ElectronicStructureMoleculeDriver,\n",
-    ")\n",
+    "from qiskit_nature.units import DistanceUnit\n",
+    "from qiskit_nature.second_q.drivers import PySCFDriver\n",
     "\n",
-    "molecule = Molecule(\n",
-    "    geometry=[[\"H\", [0.0, 0.0, 0.0]], [\"H\", [0.0, 0.0, 0.735]]], charge=0, multiplicity=1\n",
-    ")\n",
-    "driver = ElectronicStructureMoleculeDriver(\n",
-    "    molecule, basis=\"sto3g\", driver_type=ElectronicStructureDriverType.PYSCF\n",
+    "driver = PySCFDriver(\n",
+    "    atom=\"H 0 0 0; H 0 0 0.735\",\n",
+    "    basis=\"sto3g\",\n",
+    "    charge=0,\n",
+    "    spin=0,\n",
+    "    unit=DistanceUnit.ANGSTROM,\n",
     ")"
    ]
   },
@@ -156,7 +138,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from qiskit_nature.second_q.problems import ElectronicStructureProblem\n",
     "from qiskit_nature.second_q.mappers import QubitConverter\n",
     "from qiskit_nature.second_q.mappers import JordanWignerMapper, ParityMapper"
    ]
@@ -170,25 +151,19 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "  +-+- * (0.18093119978423117+0j)\n",
-      "+ +--+ * (-0.18093119978423128+0j)\n",
-      "+ -++- * (-0.18093119978423128+0j)\n",
-      "+ -+-+ * (0.18093119978423136+0j)\n",
-      "+ IIIN * (-0.4718960072811401+0j)\n",
-      "+ IINI * (-1.2563390730032502+0j)\n",
-      "+ IINN * (0.4836505304710652+0j)\n",
-      "+ INII * (-0.4718960072811401+0j)\n",
-      "+ ININ * (0.6985737227320179+0j)\n",
-      "+ INNI * (0.6645817302552963+0j)\n",
-      "+ NIII * (-1.2563390730032502+0j)\n",
-      "+ NIIN * (0.6645817302552963+0j)\n",
-      "+ NINI * (0.6757101548035165+0j)\n",
-      "+ NNII * (0.4836505304710652+0j)\n"
+      "Fermionic Operator\n",
+      "register length=4, number terms=36\n",
+      "  -1.2563390730032498 * ( +_0 -_0 )\n",
+      "+ -0.47189600728114245 * ( +_1 -_1 )\n",
+      "+ -1.2563390730032498 * ( +_2 -_2 )\n",
+      "+ -0.47189600728114245 * ( +_3 -_3 )\n",
+      "+ -0.33785507740175813 * ( +_0 +_0 -_0 -_0 )\n",
+      "+ -0. ...\n"
      ]
     }
    ],
    "source": [
-    "es_problem = ElectronicStructureProblem(driver)\n",
+    "es_problem = driver.run()\n",
     "main_op, aux_ops = es_problem.second_q_ops()\n",
     "print(main_op)"
    ]
@@ -209,21 +184,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "-0.8105479805373259 * IIII\n",
-      "- 0.2257534922240248 * ZIII\n",
-      "+ 0.17218393261915566 * IZII\n",
-      "+ 0.1209126326177663 * ZZII\n",
-      "- 0.2257534922240248 * IIZI\n",
-      "+ 0.17464343068300447 * ZIZI\n",
-      "+ 0.16614543256382408 * IZZI\n",
-      "+ 0.17218393261915566 * IIIZ\n",
-      "+ 0.16614543256382408 * ZIIZ\n",
-      "+ 0.16892753870087912 * IZIZ\n",
-      "+ 0.1209126326177663 * IIZZ\n",
-      "+ 0.04523279994605782 * XXXX\n",
-      "+ 0.04523279994605782 * YYXX\n",
-      "+ 0.04523279994605782 * XXYY\n",
-      "+ 0.04523279994605782 * YYYY\n"
+      "-0.8105479805373279 * IIII\n",
+      "+ 0.1721839326191554 * IIIZ\n",
+      "- 0.22575349222402372 * IIZI\n",
+      "+ 0.17218393261915543 * IZII\n",
+      "- 0.2257534922240237 * ZIII\n",
+      "+ 0.12091263261776627 * IIZZ\n",
+      "+ 0.16892753870087907 * IZIZ\n",
+      "+ 0.045232799946057826 * YYYY\n",
+      "+ 0.045232799946057826 * XXYY\n",
+      "+ 0.045232799946057826 * YYXX\n",
+      "+ 0.045232799946057826 * XXXX\n",
+      "+ 0.1661454325638241 * ZIIZ\n",
+      "+ 0.1661454325638241 * IZZI\n",
+      "+ 0.17464343068300453 * ZIZI\n",
+      "+ 0.12091263261776627 * ZZII\n"
      ]
     }
    ],
@@ -249,11 +224,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(-1.052373245772858+5.551115123125783e-17j) * II\n",
-      "+ (-0.39793742484318034+1.3877787807814457e-17j) * ZI\n",
-      "+ (0.3979374248431804-2.7755575615628914e-17j) * IZ\n",
-      "+ (-0.011280104256235449-1.3877787807814457e-17j) * ZZ\n",
-      "+ (0.18093119978423114-3.469446951953614e-18j) * XX\n"
+      "-1.0523732457728594 * II\n",
+      "+ 0.3979374248431778 * IZ\n",
+      "- 0.39793742484317923 * ZI\n",
+      "- 0.011280104256233658 * ZZ\n",
+      "+ 0.18093119978423122 * XX\n"
      ]
     }
    ],
@@ -285,8 +260,7 @@
     {
      "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+105cba3</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-nature</code></td><td>0.2.0</td></tr><tr><td><code>qiskit-finance</code></td><td>0.3.0</td></tr><tr><td><code>qiskit-optimization</code></td><td>0.3.0</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</td><td>3.8.10 (default, May 19 2021, 11:01:55) \n",
-       "[Clang 10.0.0 ]</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'>Mon Jul 26 13:45:29 2021 EDT</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>0.22.0.dev0+82c85d8</td></tr><tr><td><code>qiskit-aer</code></td><td>0.11.0</td></tr><tr><td><code>qiskit-ibmq-provider</code></td><td>0.20.0.dev0+4f1f8c6</td></tr><tr><td><code>qiskit-nature</code></td><td>0.5.0</td></tr><tr><th>System information</th></tr><tr><td>Python version</td><td>3.9.13</td></tr><tr><td>Python compiler</td><td>GCC 12.1.1 20220507 (Red Hat 12.1.1-1)</td></tr><tr><td>Python build</td><td>main, Jun  9 2022 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>14.845233917236328</td></tr><tr><td colspan='2'>Thu Aug 18 17:44:18 2022 CEST</td></tr></table>"
       ],
       "text/plain": [
        "<IPython.core.display.HTML object>"
@@ -298,7 +272,7 @@
     {
      "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>"
@@ -332,7 +306,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,