Fix quantity types

atomisticparsers/asap/metainfo/asap.py

@@ -16,11 +16,18 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-import numpy as np            # pylint: disable=unused-import
-import typing                 # pylint: disable=unused-import
+import numpy as np  # pylint: disable=unused-import
+import typing  # pylint: disable=unused-import
 from nomad.metainfo import (  # pylint: disable=unused-import
-    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
-    Reference
+    MSection,
+    MCategory,
+    Category,
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+    SectionProxy,
+    Reference,
 )
 import simulationworkflowschema
 
@@ -29,38 +36,40 @@
 
 
 class MolecularDynamics(simulationworkflowschema.MolecularDynamics):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_asap_langevin_friction = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         Friction coeffient used in Langevin dynamics
-        ''')
+        """,
+    )
 
     x_asap_temperature = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         Temperature used in molecular-dynamics
-        ''')
+        """,
+    )
 
     x_asap_timestep = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         Timestep in molecular dynamics
-        ''')
+        """,
+    )
 
 
 class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_asap_maxstep = Quantity(
-        type=np.dtype(np.float64),
+        type=np.float64,
         shape=[],
-        description='''
+        description="""
         Maxstep in Angstrom for geometry optimization
-        ''')
+        """,
+    )

atomisticparsers/asap/parser.py

@@ -154,9 +154,14 @@ def index():
             for constraint in traj.constraints:
                 as_dict = constraint.todict()
                 indices = as_dict["kwargs"].get("a", as_dict["kwargs"].get("indices"))
+                indices = (
+                    indices
+                    if isinstance(indices, (np.ndarray, list))
+                    else [int(indices)]
+                )
                 constraints.append(
                     dict(
-                        atom_indices=np.asarray(indices),
+                        atom_indices=[np.asarray(indices)],
                         kind=get_constraint_name(as_dict),
                     )
                 )

atomisticparsers/bopfox/metainfo/bopfox.py

@@ -16,11 +16,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-import numpy as np            # pylint: disable=unused-import
+import numpy as np  # pylint: disable=unused-import
 
 from nomad.metainfo import (  # pylint: disable=unused-import
-    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
-    Reference, JSON
+    MSection,
+    MCategory,
+    Category,
+    Package,
+    Quantity,
+    Section,
+    SubSection,
+    SectionProxy,
+    Reference,
+    JSON,
 )
 import runschema.run  # pylint: disable=unused-import
 import runschema.calculation  # pylint: disable=unused-import
@@ -32,173 +40,186 @@
 
 
 class Method(runschema.calculation.Method):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_simulation_parameters = Quantity(
         type=JSON,
         shape=[],
-        description='''
-        ''')
+        description="""
+        """,
+    )
 
 
 class Energy(runschema.calculation.Energy):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_bond = SubSection(
         sub_section=runschema.calculation.EnergyEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the bond energy.
-        ''')
+        """,
+    )
 
     x_bopfox_prom = SubSection(
         sub_section=runschema.calculation.EnergyEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the promotion energy.
-        ''')
+        """,
+    )
 
     x_bopfox_rep1 = SubSection(
         sub_section=runschema.calculation.EnergyEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the first repulsion energy.
-        ''')
+        """,
+    )
 
     x_bopfox_rep2 = SubSection(
         sub_section=runschema.calculation.EnergyEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the second repulsion energy.
-        ''')
+        """,
+    )
 
     x_bopfox_rep3 = SubSection(
         sub_section=runschema.calculation.EnergyEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the third repulsion energy.
-        ''')
+        """,
+    )
 
 
 class Forces(runschema.calculation.Forces):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_analytic = SubSection(
         sub_section=runschema.calculation.ForcesEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the analytic forces.
-        ''')
+        """,
+    )
 
     x_bopfox_rep1 = SubSection(
         sub_section=runschema.calculation.ForcesEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the first analytic forces.
-        ''')
+        """,
+    )
 
     x_bopfox_rep2 = SubSection(
         sub_section=runschema.calculation.ForcesEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the second analytic forces.
-        ''')
+        """,
+    )
 
     x_bopfox_rep3 = SubSection(
         sub_section=runschema.calculation.ForcesEntry.m_def,
-        description='''
+        description="""
         Contains the value and information regarding the third analytic forces.
-        ''')
+        """,
+    )
 
 
 class x_bopfox_onsite_levels_value(runschema.calculation.AtomicValues):
-
     m_def = Section(validate=False)
 
     value = Quantity(
         type=np.dtype(np.float64),
         shape=[],
-        description='''
+        description="""
         Value of the onsite level projected on orbital and spin channel.
-        ''')
+        """,
+    )
 
 
 class x_bopfox_onsite_levels(runschema.calculation.Atomic):
-
     m_def = Section(validate=False)
 
-    orbital_projected = SubSection(sub_section=x_bopfox_onsite_levels_value.m_def, repeats=True)
+    orbital_projected = SubSection(
+        sub_section=x_bopfox_onsite_levels_value.m_def, repeats=True
+    )
 
 
 class Calculation(runschema.calculation.Calculation):
-
     m_def = Section(validate=False, extends_base_section=True)
 
-    x_bopfox_onsite_levels = SubSection(sub_section=x_bopfox_onsite_levels.m_def, repeats=True)
+    x_bopfox_onsite_levels = SubSection(
+        sub_section=x_bopfox_onsite_levels.m_def, repeats=True
+    )
 
 
 class Interaction(runschema.method.Interaction):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_valence = Quantity(
         type=str,
-        shape=['n_atoms'],
-        description='''
+        shape=["n_atoms"],
+        description="""
         Valence of the atoms described by the interaction.
-        ''')
+        """,
+    )
 
     x_bopfox_chargetransfer = Quantity(
         type=np.dtype(np.float64),
-        shape=[],
-        description='''
+        shape=["*"],
+        description="""
         Charge transfer parameters.
-        ''')
+        """,
+    )
 
     x_bopfox_cutoff = Quantity(
         type=np.dtype(np.float64),
         shape=[],
-        description='''
+        description="""
         Cutoff distance for the interaction.
-        ''')
+        """,
+    )
 
     x_bopfox_dcutoff = Quantity(
         type=np.dtype(np.float64),
         shape=[],
-        description='''
+        description="""
         Distance from cutoff where the cutoff function is applied.
-        ''')
+        """,
+    )
 
 
 class Model(runschema.method.Model):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_parameters = Quantity(
         type=JSON,
         shape=[],
-        description='''
-        ''')
+        description="""
+        """,
+    )
 
 
 class xTB(runschema.method.xTB):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_parameters = Quantity(
         type=JSON,
         shape=[],
-        description='''
-        ''')
+        description="""
+        """,
+    )
 
 
 class AtomParameters(runschema.method.AtomParameters):
-
     m_def = Section(validate=False, extends_base_section=True)
 
     x_bopfox_valenceorbitals = Quantity(
         type=np.dtype(np.int32),
         shape=[],
-        description='''
-        ''')
+        description="""
+        """,
+    )
 
     x_bopfox_stonerintegral = Quantity(
         type=np.dtype(np.float64),
         shape=[3],
-        description='''
-        ''')
+        description="""
+        """,
+    )

atomisticparsers/bopfox/parser.py

@@ -469,7 +469,7 @@ def write_to_archive(self) -> None:
                                         name=key,
                                         functional_form=val[0],
                                         parameters=val[1:],
-                                        atom_labels=bond.get("bond"),
+                                        atom_labels=[bond.get("bond")],
                                         x_bopfox_valence=bond.get("valence"),
                                         x_bopfox_cutoff=bond.get("rcut"),
                                         x_bopfox_dcutoff=bond.get("dcut"),
@@ -496,7 +496,7 @@ def write_to_archive(self) -> None:
                                         name=key,
                                         functional_form=val[0],
                                         parameters=val[1:],
-                                        atom_labels=bond.get("bond"),
+                                        atom_labels=[bond.get("bond")],
                                         x_bopfox_cutoff=bond.get("r2cut"),
                                         x_bopfox_dcutoff=bond.get("d2cut"),
                                     )
@@ -508,7 +508,7 @@ def write_to_archive(self) -> None:
                                         name=key,
                                         functional_form=val[0],
                                         parameters=val[1:],
-                                        atom_labels=bond.get("bond"),
+                                        atom_labels=[bond.get("bond")],
                                         x_bopfox_cutoff=bond.get("r2cut"),
                                         x_bopfox_dcutoff=bond.get("d2cut"),
                                     )