fix tests and fucntional references

Co-authored-by: Copilot <copilot@github.com>

Author: Sathya-S3

src/nomad_parser_magres/parsers/parser.py

@@ -544,7 +544,7 @@ def parse_xc_functional(
         xc_functional_labels = self._xc_functional_map.get(xc_functional, [])
         xc_sections = []
         for xc in xc_functional_labels:
-            functional = XCFunctional(libxc_name=xc)
+            functional = XCFunctional(functional_key=xc)
             if '_X_' in xc:
                 functional.name = 'exchange'
             elif '_C_' in xc:
@@ -1182,15 +1182,11 @@ def parse_outputs(
             model_method_ref=simulation.model_method[-1],
             model_system_ref=simulation.model_system[-1],
         )
-        if (
-            not simulation.model_system[-1].cell
-            or not simulation.model_system[-1].particle_states
-        ):
+        if not simulation.model_system[-1].particle_states:
             logger.warning(
-                'Could not find the `cell` sub-section or the `MagresParser.atom_state_class` list under particle states.'
+                'Could not find the `MagresParser.atom_state_class` list under particle states.'
             )
             return None
-        cell = simulation.model_system[-1].cell[-1]
 
         # Check if [magres][/magres] was correctly parsed
         magres_data = self.magres_file_parser.get('magres')

tests/test_parser.py

@@ -49,22 +49,18 @@ def test_single_point_ethanol(parser):
     for index, label in enumerate(labels):
         assert model_system.particle_states[index].label == label
 
-    # Cell
-    assert len(model_system.cell) == 1
-    atomic_cell = model_system.cell[0]
-
-    # Lattice vectors: atomic_cell.lattice_vectors is a numpy array (or Quantity) of shape (3, 3)
+    # Lattice vectors: model_system.lattice_vectors is a numpy array (or Quantity) of shape (3, 3)
     expected_lattice = np.array(
         [
             [6.0, 0.0, 0.0],
             [0.0, 6.0, 0.0],
             [0.0, 0.0, 6.0],
         ]
     )
-    lattice_vectors = atomic_cell.lattice_vectors.to('angstrom').magnitude
+    lattice_vectors = model_system.lattice_vectors.to('angstrom').magnitude
     assert np.allclose(lattice_vectors, expected_lattice, atol=1e-8)
 
-    assert atomic_cell.periodic_boundary_conditions == [True, True, True]
+    assert model_system.periodic_boundary_conditions == [True, True, True]
 
     # ModelMethod
     assert len(simulation.model_method) == 1
@@ -75,9 +71,9 @@ def test_single_point_ethanol(parser):
     assert len(dft.xc_functionals) == 2
     # Order is correlation then exchange for PBE in the parser map
     assert dft.xc_functionals[0].name == 'correlation'
-    assert dft.xc_functionals[0].libxc_name == 'GGA_C_PBE'
+    assert dft.xc_functionals[0].functional_key == 'GGA_C_PBE'
     assert dft.xc_functionals[1].name == 'exchange'
-    assert dft.xc_functionals[1].libxc_name == 'GGA_X_PBE'
+    assert dft.xc_functionals[1].functional_key == 'GGA_X_PBE'
     # NumericalSettings
     assert len(dft.numerical_settings) == 1
     k_space = dft.numerical_settings[0]