Merge branch 'fix_release_issues' of https://github.com/qiboteam/qibo…

…chem into fix_release_issues

doc/source/conf.py

@@ -136,7 +136,7 @@ def setup(app):
     app.add_css_file("css/style.css")
     # Register a sphinx.ext.autodoc.between listener to ignore everything
     # between lines that contain the word IGNORE
-    app.connect('autodoc-process-docstring', between('^.*IGNORE.*$', exclude=True))
+    app.connect("autodoc-process-docstring", between("^.*IGNORE.*$", exclude=True))
     return app
 
 

src/qibochem/driver/molecule.py

@@ -374,7 +374,7 @@ def hamiltonian(
         if ham_type in ("s", "sym"):
             # Qibo SymbolicHamiltonian
             return symbolic_hamiltonian(ham)
-        raise NameError(f"Unknown {ham_type}!")  # Shouldn't ever reach here
+        # raise NameError(f"Unknown {ham_type}!")  # Shouldn't ever reach here
 
     @staticmethod
     def eigenvalues(hamiltonian):

tests/data/h2.xyz

@@ -0,0 +1,4 @@
+2
+
+H 0.0 0.0 0.0
+H 0.0 0.0 0.7

tests/data/lih.xyz

@@ -0,0 +1,4 @@
+2
+0 1
+Li 0.0 0.0 0.0
+H 0.0 0.0 1.2

tests/test_molecule.py

@@ -29,18 +29,59 @@ def test_run_pyscf():
 
 def test_run_pyscf_molecule_xyz():
     """Pyscf driver with xyz file"""
-    path = "./lih.xyz"
+    path = "./tests/data/lih.xyz"
     check_file = os.path.exists(path)
     if check_file == False:
-        with open("lih.xyz", "a") as file:
+        with open("./tests/data/lih.xyz", "a") as file:
             file.write("2\n 0 1\n Li 0.0 0.0 0.0\n H 0.0 0.0 1.2")
     lih_ref_energy = -7.83561582555692
-    lih = Molecule(xyz_file="lih.xyz")
+    lih = Molecule(xyz_file="./tests/data/lih.xyz")
     lih.run_pyscf()
 
     assert lih.e_hf == pytest.approx(lih_ref_energy)
 
 
+def test_run_pyscf_molecule_xyz_charged():
+    path = "./tests/data/h2.xyz"
+    check_file = os.path.exists(path)
+    if check_file == False:
+        with open("./tests/data/h2.xyz", "a") as file:
+            file.write("2\n \n H 0.0 0.0 0.0\n H 0.0 0.0 0.7")
+    h2_ref_energy = -1.117349035
+    h2 = Molecule(xyz_file="./tests/data/h2.xyz")
+    h2.run_pyscf()
+
+    assert h2.e_hf == pytest.approx(h2_ref_energy)
+
+
+def test_molecule_custom_basis():
+    mol = Molecule([("Li", (0.0, 0.0, 0.0)), ("H", (0.0, 0.0, 1.2))], 0, 1, "6-31g")
+    mol.run_pyscf()
+    assert np.isclose(mol.e_hf, -7.94129296352493)
+
+
+def test_hf_embedding_1():
+    mol = Molecule([("Li", (0.0, 0.0, 0.0)), ("H", (0.0, 0.0, 1.2))])
+    mol.run_pyscf()
+    ref_oei = mol.oei
+    ref_tei = mol.tei
+    mol.hf_embedding()
+    embed_oei = mol.embed_oei
+    embed_tei = mol.embed_tei
+    assert np.allclose(embed_oei, ref_oei)
+    assert np.allclose(embed_tei, ref_tei)
+
+
+def test_hf_embedding_2():
+    mol = Molecule([("Li", (0.0, 0.0, 0.0)), ("H", (0.0, 0.0, 1.2))])
+    mol.run_pyscf()
+    mol.frozen = [0]
+    mol.active = [1, 2]
+    mol.hf_embedding()
+    assert mol.n_active_orbs == 4
+    assert mol.n_active_e == 2
+
+
 def test_fermionic_hamiltonian():
     h2 = Molecule([("H", (0.0, 0.0, 0.0)), ("H", (0.0, 0.0, 0.7))])
     h2.run_pyscf()