More fixes

nomad-coe · Apr 25, 2024 · d8360f0 · d8360f0
1 parent 7ff8e6f
commit d8360f0
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Showing 3 changed files with 56 additions and 54 deletions.
diff --git a/atomisticparsers/dlpoly/parser.py b/atomisticparsers/dlpoly/parser.py
@@ -153,7 +153,7 @@ def to_bonds(val_in):
                     dict(
                         functional_form=potentials.get(val_n[0], val_n[0]),
                         # atom index starts from 1
-                        atom_indices=[int(n) - 1 for n in val_n[1:3]],
+                        atom_indices=[[int(n) - 1 for n in val_n[1:3]]],
                         parameters=[float(v) for v in val_n[3:]],
                     )
                 )
@@ -180,7 +180,7 @@ def to_angles(val_in):
                 interactions.append(
                     dict(
                         functional_form=potentials.get(val_n[0], val_n[0]),
-                        atom_indices=[int(n) - 1 for n in val_n[1:4]],
+                        atom_indices=[[int(n) - 1 for n in val_n[1:4]]],
                         parameters=[float(v) for v in val_n[4:]],
                     )
                 )
@@ -202,7 +202,7 @@ def to_dihedrals(val_in):
                 interactions.append(
                     dict(
                         functional_form=potentials.get(val_n[0], val_n[0]),
-                        atom_indices=[int(n) - 1 for n in val_n[1:5]],
+                        atom_indices=[[int(n) - 1 for n in val_n[1:5]]],
                         parameters=[float(v) for v in val_n[5:]],
                     )
                 )
@@ -221,7 +221,7 @@ def to_inversions(val_in):
                 interactions.append(
                     dict(
                         functional_form=potentials.get(val_n[0], val_n[0]),
-                        atom_indices=[int(n) - 1 for n in val_n[1:5]],
+                        atom_indices=[[int(n) - 1 for n in val_n[1:5]]],
                         parameters=[float(v) for v in val_n[5:]],
                     )
                 )
@@ -235,7 +235,7 @@ def to_teth(val_in):
                 interactions.append(
                     dict(
                         functional_form=potentials.get(val_n[0], val_n[0]),
-                        atom_indices=[int(n) - 1 for n in val_n[1:2]],
+                        atom_indices=[[int(n) - 1 for n in val_n[1:2]]],
                         parameters=[float(v) for v in val_n[2:]],
                     )
                 )
@@ -377,7 +377,7 @@ def to_metal(val_in):
                             convert=False,
                             str_operation=lambda x: [
                                 dict(
-                                    atom_indices=[int(v) - 1 for v in val[:2]],
+                                    atom_indices=[[int(v) - 1 for v in val[:2]]],
                                     parameters=[float(v) for v in val[2:3]],
                                 )
                                 for val in [v.split() for v in x.strip().splitlines()]
@@ -649,14 +649,16 @@ def get_system_data(frame_index):
                     sec_interaction = Interaction()
                     sec_model.contributions.append(sec_interaction)
                     for key, val in interaction.items():
-                        setattr(sec_interaction, key, val)
+                        sec_interaction.m_set(
+                            sec_interaction.m_get_quantity_definition(key), val
+                        )
             # add constraints to initial system
             constraint_data = []
             for constraint in molecule.get("constraints", []):
                 constraint_data.append(
                     dict(
                         kind="fixed bond length",
-                        atom_indices=[constraint.get("atom_indices")],
+                        atom_indices=constraint.get("atom_indices"),
                         parameters=constraint.get("parameters"),
                     )
                 )