New ModelSystem schema

nomad-coe · Dec 18, 2023 · 09b9430 · 09b9430
1 parent 9452d25
commit 09b9430
Showing 1 changed file with 11 additions and 11 deletions.
diff --git a/electronicparsers/wannier90/parser.py b/electronicparsers/wannier90/parser.py
@@ -37,7 +37,7 @@
 # New schema
 from nomad.datamodel.metainfo.basesections import Program as BaseProgram
 from nomad.datamodel.metainfo.computation import Computation
-from nomad.datamodel.metainfo.computation.system import ModelSystem, Atoms as Atoms2, SystemGroups
+from nomad.datamodel.metainfo.computation.system import ModelSystem, AtomicCell
 
 
 re_n = r'[\n\r]'
@@ -220,7 +220,7 @@ def parse_system(self, sec_computation):
             return
 
         sec_atoms = sec_system.m_create(Atoms)
-        sec_atoms2 = sec_system2.m_create(Atoms2)
+        sec_atoms2 = sec_system2.m_create(AtomicCell)
         if self.wout_parser.get('lattice_vectors', []):
             lattice_vectors = np.vstack(self.wout_parser.get('lattice_vectors', [])[-3:])
             sec_atoms.lattice_vectors = lattice_vectors * ureg.angstrom
@@ -352,8 +352,8 @@ def fract_cart_sites(sec_atoms, units, val):
     def parse_winput2(self, sec_computation):
         sec_run = sec_computation
         try:
-            sec_system = sec_run.system[-1]
-            sec_atoms = sec_system.atoms[0]
+            sec_system = sec_run.model_system[-1]
+            sec_atoms = sec_system.atomic_cell[0]
         except Exception:
             self.logger.warning('Could not extract system.atoms and method sections for parsing win.')
             return
@@ -388,10 +388,10 @@ def fract_cart_sites(sec_atoms, units, val):
 
         # Populating AtomsGroup for projected atoms
         for nat in range(len(projections)):
-            sec_atoms_group = sec_system.m_create(SystemGroups)
-            sec_atoms_group.type = 'projected_atom'
+            sec_atoms_group = sec_system.m_create(ModelSystem)
+            sec_atoms_group.type = 'active_atom'
             # sec_atoms_group.index = 0  # Always first index (projection on a projection does not exist)
-            sec_atoms_group.is_molecule = False
+            # sec_atoms_group.is_molecule = False
 
             # atom label always index=0
             try:
@@ -405,10 +405,10 @@ def fract_cart_sites(sec_atoms, units, val):
                     sites = fract_cart_sites(sec_atoms, x_wannier90_units, val)
                 else:  # atom label directly specified
                     sites = atom
-                sec_atoms_group.n_entities = len(sites)  # always 1 (only one atom per proj)
-                sec_atoms_group.label = sites
-                sec_atoms_group.entity_indices = np.where([
-                    x == sec_atoms_group.label for x in sec_atoms.labels])[0]
+                # sec_atoms_group.n_entities = len(sites)  # always 1 (only one atom per proj)
+                sec_atoms_group.tree_label = sites
+                sec_atoms_group.atom_indices = np.where([
+                    x == sec_atoms_group.tree_label for x in sec_atoms.labels])[0]
             except Exception:
                 self.logger.warning('Error finding the atom labels for the projection from win.')