updated force and energy contributions

src/nomad_simulations/outputs.py

@@ -16,6 +16,7 @@
 # limitations under the License.
 #
 
+import numpy as np
 from structlog.stdlib import BoundLogger
 from typing import Optional, List
 
@@ -308,13 +309,13 @@ class WorkflowOutputs(Outputs):
         """,
     )
 
-    workflow_ref = Quantity(
-        type=SimulationWorkflow,
-        description="""
-        Reference to the `SelfConsistency` section that defines the numerical settings to converge the
-        output property.
-        """,
-    )
+    # workflow_ref = Quantity(
+    #     type=SimulationWorkflow,
+    #     description="""
+    #     Reference to the `SelfConsistency` section that defines the numerical settings to converge the
+    #     output property.
+    #     """,
+    # )
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)

src/nomad_simulations/properties/__init__.py

@@ -16,7 +16,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .energies import FermiLevel, ChemicalPotential, TotalEnergy
+from .energies import (
+    FermiLevel,
+    ChemicalPotential,
+    TotalEnergy,
+    ClassicalEnergyContributions,
+    QuantumEnergyContributions,
+)
 from .band_gap import ElectronicBandGap
 from .spectral_profile import (
     SpectralProfile,

src/nomad_simulations/properties/energies.py

@@ -296,7 +296,7 @@ class ExternalEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
-class ClassicalEnergyContributions(PhysicalProperty):
+class ClassicalEnergyContributions(ArchiveSection):
     """
     Section containing contributions to the potential energy from a classical force field.
     """
@@ -451,7 +451,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class T0Energy(PhysicalProperty):
+class ZeroTemperatureEnergy(PhysicalProperty):
     """
     Section containing the total energy of a (sub)system extrapolated to $T=0$.
     """
@@ -520,7 +520,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class QuantumEnergyContributions(EnergyContributions):
+class QuantumEnergyContributions(ArchiveSection):
     """
     Section containing contributions to the potential energy from a DFT calculation.
     """
@@ -538,7 +538,7 @@ class QuantumEnergyContributions(EnergyContributions):
 
     exchange = SubSection(sub_section=ExchangeEnergy.m_def, repeats=False)
 
-    t0 = SubSection(sub_section=T0Energy.m_def, repeats=False)
+    zero_temperature = SubSection(sub_section=ZeroTemperatureEnergy.m_def, repeats=False)
 
     zero_point = SubSection(sub_section=ZeroPointEnergy.m_def, repeats=False)
 

src/nomad_simulations/properties/forces.py

@@ -69,113 +69,128 @@
 
 from .model_system import ModelSystem
 
+################################
+# List of Forces Contributions #
+################################
 
-
-class ForceTotal(PhysicalProperty):
+class FreeForce(PhysicalProperty):
     """
-    Section containing the total force of a (sub)system.
+    Contains the value and information regarding the forces on the atoms
+    corresponding to the minus gradient of energy_free. The (electronic) energy_free
+    contains the information on the change in (fractional) occupation of the
+    electronic eigenstates, which are accounted for in the derivatives, yielding a
+    truly energy-conserved quantity.
     """
 
     value = Quantity(
-        type=np.float64,
+        type=np.dtype(np.float64),
+        shape=['n_atoms', 3],
         unit='newton',
         description="""
-        The value of the total force.
+        The value of the free force.
         """,
     )
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
-
-
-class ForcesEntry(Atomic):
+class ZeroTemperatureForce(PhysicalProperty):
     """
-    Section describing a contribution to or type of atomic forces.
+    Contains the value and information regarding the forces on the atoms
+    corresponding to the minus gradient of energy_T0.
     """
 
-    m_def = Section(validate=False)
-
     value = Quantity(
         type=np.dtype(np.float64),
         shape=['n_atoms', 3],
         unit='newton',
         description="""
-        Value of the forces acting on the atoms. This is calculated as minus gradient of
-        the corresponding energy type or contribution **including** constraints, if
-        present. The derivatives with respect to displacements of nuclei are evaluated in
-        Cartesian coordinates.  In addition, these are obtained by filtering out the
-        unitary transformations (center-of-mass translations and rigid rotations for
-        non-periodic systems, see value_raw for the unfiltered counterpart).
+        The value of the free force.
         """,
     )
 
-    value_raw = Quantity(
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class RawForce(PhysicalProperty):
+    """
+    """
+
+    value = Quantity(
         type=np.dtype(np.float64),
         shape=['n_atoms', 3],
         unit='newton',
         description="""
         Value of the forces acting on the atoms **not including** such as fixed atoms,
-        distances, angles, dihedrals, etc.""",
+        distances, angles, dihedrals, etc.
+        """,
+        # ? This is VERY imprecise, is this used regularly?
     )
-    # ? This is VERY imprecise, is this used regularly?
 
-class Forces(MSection):
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+    #? Do we want to support custom contributions?
+    # contributions = SubSection(
+    #     sub_section=ForcesEntry.m_def,
+    #     description="""
+    #     Contains other forces contributions to the total atomic forces not already
+    #     defined.
+    #     """,
+    #     repeats=True,
+    # )
+
+    # types = SubSection(
+    #     sub_section=ForcesEntry.m_def,
+    #     description="""
+    #     Contains other types of forces not already defined.
+    #     """,
+    #     repeats=True,
+    # )
+
+class ForceContributions(ArchiveSection):
     """
-    Section containing all forces types and contributions.
+    Section containing contributions to the potential energy from a classical force field.
     """
 
-    m_def = Section(validate=False)
+    free = SubSection(sub_section=FreeForce.m_def, repeats=False)
 
-    total = SubSection(
-        sub_section=ForcesEntry.m_def,
-        description="""
-        Contains the value and information regarding the total forces on the atoms
-        calculated as minus gradient of energy_total.
-        """,
-    )
-    # ! We need to avoid giving the precise method of calculation without also providing context, this is not necessarily true in general!
+    zero_temperature_force = SubSection(sub_section=ZeroTemperatureForce.m_def, repeats=False)
 
-    free = SubSection(
-        sub_section=ForcesEntry.m_def,
-        description="""
-        Contains the value and information regarding the forces on the atoms
-        corresponding to the minus gradient of energy_free. The (electronic) energy_free
-        contains the information on the change in (fractional) occupation of the
-        electronic eigenstates, which are accounted for in the derivatives, yielding a
-        truly energy-conserved quantity.
-        """,
-    )
+    raw = SubSection(sub_section=RawForce.m_def, repeats=False)
 
-    t0 = SubSection(
-        sub_section=ForcesEntry.m_def,
-        description="""
-        Contains the value and information regarding the forces on the atoms
-        corresponding to the minus gradient of energy_T0.
-        """,
-    )
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+        self.name = self.m_def.name
 
-    contributions = SubSection(
-        sub_section=ForcesEntry.m_def,
-        description="""
-        Contains other forces contributions to the total atomic forces not already
-        defined.
-        """,
-        repeats=True,
-    )
 
-    types = SubSection(
-        sub_section=ForcesEntry.m_def,
+# Old version of the Forces description
+        # Value of the forces acting on the atoms. This is calculated as minus gradient of
+        # the corresponding energy type or contribution **including** constraints, if
+        # present. The derivatives with respect to displacements of nuclei are evaluated in
+        # Cartesian coordinates.  In addition, these are obtained by filtering out the
+        # unitary transformations (center-of-mass translations and rigid rotations for
+        # non-periodic systems, see value_raw for the unfiltered counterpart).
+class TotalForce(PhysicalProperty):
+    """
+    Section containing the total force of a (sub)system.
+
+    Contains the value and information regarding the total forces on the atoms
+    calculated as minus gradient of energy_total.
+    """
+    # ! We need to avoid giving the precise method of calculation without also providing context, this is not necessarily true in general!
+
+    value = Quantity(
+        type=np.float64,
+        unit='newton',
         description="""
-        Contains other types of forces not already defined.
+        The value of the total force.
         """,
-        repeats=True,
     )
 
+    force_contributions = SubSection(sub_section=ForceContributions.m_def, repeats=False)
+    #? Do we need to separate classical and quantum contributions here?
 
-
-
-
-    forces = SubSection(sub_section=Forces.m_def)
-
-
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)