Merge branch 'main' into dev/docs

.github/.codecov.yml

@@ -0,0 +1,4 @@
+# Reference docs at https://docs.codecov.com/docs/codecovyml-reference
+
+codecov:
+  require_ci_to_pass: yes

.github/workflows/tests.yml

@@ -14,5 +14,5 @@ jobs:
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      poetry-extras: "--with docs,tests,analysis --all-extras"
+      poetry-extras: --with docs,tests,analysis --all-extras
     secrets: inherit

.pre-commit-config.yaml

@@ -20,6 +20,6 @@ repos:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.9.0
+    rev: v3.10.1
     hooks:
       - id: pyupgrade

pyproject.toml

@@ -15,10 +15,11 @@ classifiers = [
 packages = [{ include = "qibochem", from = "src" }]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = ">3.9,<3.12"
 qibo = "^0.1.10"
 openfermion = "^1.5"
-pyscf = "^2.2.1"
+pyscf = "^2.3.0"
+scipy = "^1.10.1"
 
 [build-system]
 requires = ["poetry-core"]

src/qibochem/driver/molecule.py

@@ -385,56 +385,6 @@ def hamiltonian(
             return ham_type  # Yummy!
         raise NameError(f"Unknown {ham_type}!")  # Shouldn't ever reach here
 
-    @staticmethod
-    def expectation(
-        circuit: qibo.models.Circuit, hamiltonian: SymbolicHamiltonian, from_samples=False, n_shots=1000
-    ) -> float:
-        """
-        Calculate expectation value of Hamiltonian using either the state vector from running a
-            circuit, or the frequencies of the resultant binary string results
-
-        Args:
-            circuit (qibo.models.Circuit): Quantum circuit ansatz
-
-            hamiltonian (SymbolicHamiltonian): Molecular Hamiltonian
-
-            from_samples: Whether the expectation value calculation uses samples or the simulated
-
-            state vector. Default: False, state vector simulation
-
-            n_shots: Number of times the circuit is run for the from_samples=True case
-
-        Returns:
-            Hamiltonian expectation value (float)
-        """
-        if from_samples:
-            raise NotImplementedError("expectation function only works with state vector")
-        # TODO: Rough code for expectation_from_samples if issue resolved
-        # Yet to test!!!!!
-        #
-        # from functools import reduce
-        # total = 0.0
-        # Iterate over each term in the Hamiltonian
-        # for term in hamiltonian.terms:
-        #     # Get the basis rotation gates and target qubits from the Hamiltonian term
-        #     qubits = [factor.target_qubit for factor in term.factors]
-        #     basis = [type(factor.gate) for factor in term.factors]
-        #     # Run a copy of the initial circuit to get the output frequencies
-        #     _circuit = circuit.copy()
-        #     _circuit.add(gates.M(*qubits, basis=basis))
-        #     result = _circuit(nshots=n_shots)
-        #     frequencies = result.frequencies(binary=True)
-        #     # Only works for Z terms, raises an error if ham_term has X/Y terms
-        #     total += SymbolicHamiltonian(
-        #                  reduce(lambda x, y: x*y, term.factors, 1)
-        #              ).expectation_from_samples(frequencies, qubit_map=qubits)
-        # return total
-
-        # Expectation value from state vector simulation
-        result = circuit(nshots=1)
-        state_ket = result.state()
-        return hamiltonian.expectation(state_ket)
-
     @staticmethod
     def eigenvalues(hamiltonian):
         """

src/qibochem/measurement/expectation.py

@@ -1,6 +1,9 @@
 # from qibo import gates
 # from qibo.models import Circuit
 
+import qibo
+from qibo.hamiltonians import SymbolicHamiltonian
+
 from qibochem.measurement.basis_rotate import measure_rotate_basis
 
 
@@ -67,3 +70,49 @@ def circuit_expectation_shots(qc, of_qubham, nshots=1000):
         istring += 1
 
     return expectation
+
+
+def expectation(
+    circuit: qibo.models.Circuit, hamiltonian: SymbolicHamiltonian, from_samples=False, n_shots=1000
+) -> float:
+    """
+    Calculate expectation value of Hamiltonian using either the state vector from running a
+        circuit, or the frequencies of the resultant binary string results
+
+    Args:
+        circuit (qibo.models.Circuit): Quantum circuit ansatz
+        hamiltonian (SymbolicHamiltonian): Molecular Hamiltonian
+        from_samples: Whether the expectation value calculation uses samples or the simulated
+            state vector. Default: False, state vector simulation
+        n_shots: Number of times the circuit is run for the from_samples=True case
+
+    Returns:
+        Hamiltonian expectation value (float)
+    """
+    if from_samples:
+        raise NotImplementedError("expectation function only works with state vector")
+    # TODO: Rough code for expectation_from_samples if issue resolved
+    # Yet to test!!!!!
+    #
+    # from functools import reduce
+    # total = 0.0
+    # Iterate over each term in the Hamiltonian
+    # for term in hamiltonian.terms:
+    #     # Get the basis rotation gates and target qubits from the Hamiltonian term
+    #     qubits = [factor.target_qubit for factor in term.factors]
+    #     basis = [type(factor.gate) for factor in term.factors]
+    #     # Run a copy of the initial circuit to get the output frequencies
+    #     _circuit = circuit.copy()
+    #     _circuit.add(gates.M(*qubits, basis=basis))
+    #     result = _circuit(nshots=n_shots)
+    #     frequencies = result.frequencies(binary=True)
+    #     # Only works for Z terms, raises an error if ham_term has X/Y terms
+    #     total += SymbolicHamiltonian(
+    #                  reduce(lambda x, y: x*y, term.factors, 1)
+    #              ).expectation_from_samples(frequencies, qubit_map=qubits)
+    # return total
+
+    # Expectation value from state vector simulation
+    result = circuit(nshots=1)
+    state_ket = result.state()
+    return hamiltonian.expectation(state_ket)

tests/test_hf_circuit.py

@@ -7,6 +7,7 @@
 
 from qibochem.ansatz.hf_reference import hf_circuit
 from qibochem.driver.molecule import Molecule
+from qibochem.measurement.expectation import expectation
 
 
 def test_jw_circuit():
@@ -25,7 +26,7 @@ def test_jw_circuit():
 
     # Molecular Hamiltonian and the HF expectation value
     hamiltonian = h2.hamiltonian()
-    hf_energy = h2.expectation(circuit, hamiltonian)
+    hf_energy = expectation(circuit, hamiltonian)
 
     # assert h2.e_hf == pytest.approx(hf_energy)
     assert h2_ref_energy == pytest.approx(hf_energy)
@@ -47,7 +48,7 @@ def test_bk_circuit_1():
 
     # Molecular Hamiltonian and the HF expectation value
     hamiltonian = h2.hamiltonian(ferm_qubit_map="bk")
-    hf_energy = h2.expectation(circuit, hamiltonian)
+    hf_energy = expectation(circuit, hamiltonian)
 
     # assert h2.e_hf == pytest.approx(hf_energy)
     assert h2_ref_energy == pytest.approx(hf_energy)
@@ -67,6 +68,6 @@ def test_bk_circuit_2():
 
     # Molecular Hamiltonian and the HF expectation value
     hamiltonian = lih.hamiltonian(ferm_qubit_map="bk")
-    hf_energy = lih.expectation(circuit, hamiltonian)
+    hf_energy = expectation(circuit, hamiltonian)
 
     assert lih.e_hf == pytest.approx(hf_energy)

tests/test_molecule.py

@@ -7,6 +7,7 @@
 from qibo import gates, models
 
 from qibochem.driver.molecule import Molecule
+from qibochem.measurement.expectation import expectation
 
 
 def test_run_pyscf():
@@ -52,7 +53,7 @@ def test_expectation_value():
     circuit.add(gates.X(_i) for _i in range(sum(h2.nelec)))
     # Molecular Hamiltonian and the HF expectation value
     hamiltonian = h2.hamiltonian()
-    hf_energy = h2.expectation(circuit, hamiltonian)
+    hf_energy = expectation(circuit, hamiltonian)
 
     # assert h2.e_hf == pytest.approx(hf_energy)
     assert h2_ref_energy == pytest.approx(hf_energy)