updated force to new structure

nomad-coe · Jun 21, 2024 · 353ca15 · 353ca15
1 parent 1a0fc7b
commit 353ca15
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diff --git a/src/nomad_simulations/properties/__init__.py b/src/nomad_simulations/properties/__init__.py
@@ -20,10 +20,11 @@
     FermiLevel,
     ChemicalPotential,
     TotalEnergy,
-    ClassicalEnergyContributions,
-    QuantumEnergyContributions,
+    Energy,
+    ClassicalEnergy,
+    QuantumEnergy,
 )
-from .forces import TotalForce, ForceContributions
+from .forces import TotalForce, Force
 from .band_gap import ElectronicBandGap
 from .spectral_profile import (
     SpectralProfile,

diff --git a/src/nomad_simulations/properties/energies.py b/src/nomad_simulations/properties/energies.py
@@ -131,7 +131,7 @@ def normalize(self, archive, logger) -> None:
                 f"Misidentified type for classical energy."
             )
 
-class QuamtumEnergy(Energy):
+class QuantumEnergy(Energy):
     """
     Abstract physical property section describing some quantum energy of a (sub)system.
     """
@@ -300,7 +300,7 @@ def normalize(self, archive, logger) -> None:
 # List of quantum energy contributions
 ######################################
 
-class ElectronicEnergy(QuamtumEnergy):
+class ElectronicEnergy(QuantumEnergy):
     """
     Physical property section describing the electronic energy of a (sub)system.
     """
@@ -310,7 +310,7 @@ def normalize(self, archive, logger) -> None:
 #! allowed_contributions = ['PotKin'] Not sure how to deal with sub-contributions... - I lean towards keeping a flat list but I am not sure of all the usages
 
 
-class ElectronicKineticEnergy(QuamtumEnergy):
+class ElectronicKineticEnergy(QuantumEnergy):
     """
     Physical property section describing the electronic kinetic energy of a (sub)system.
     """
@@ -319,7 +319,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class XCEnergy(QuamtumEnergy):
+class XCEnergy(QuantumEnergy):
     """
     Physical property section describing the exchange-correlation (XC) energy of a (sub)system,
     calculated using the functional stored in XC_functional.
@@ -331,7 +331,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class XCPotentialEnergy(QuamtumEnergy):
+class XCPotentialEnergy(QuantumEnergy):
     """
     Physical property section describing the potential energy contribution to the exchange-correlation (XC) energy,
     i.e., the integral of the first order derivative of the functional
@@ -347,7 +347,7 @@ def normalize(self, archive, logger) -> None:
 
 
 # ? XCCorrelationEnergy?
-class CorrelationEnergy(QuamtumEnergy):
+class CorrelationEnergy(QuantumEnergy):
     """
     Physical property section describing the correlation energy of a (sub)system,
     calculated using the method described in XC_functional.
@@ -369,7 +369,7 @@ def normalize(self, archive, logger) -> None:
 
 
 # ? XCExchangeEnergy?
-class ExchangeEnergy(QuamtumEnergy):
+class ExchangeEnergy(QuantumEnergy):
     """
     Physical property section describing the exchange energy of a (sub)system,
     calculated using the method described in XC_functional.
@@ -381,7 +381,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class ZeroTemperatureEnergy(QuamtumEnergy):
+class ZeroTemperatureEnergy(QuantumEnergy):
     """
     Physical property section describing the total energy of a (sub)system extrapolated to $T=0$, based on a free-electron gas argument.
     """
@@ -392,7 +392,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class ZeroPointEnergy(QuamtumEnergy):
+class ZeroPointEnergy(QuantumEnergy):
     """
     Physical property section describing the zero-point vibrational energy of a (sub)system,
     calculated using the method described in zero_point_method.
@@ -404,7 +404,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class ElectrostaticEnergy(QuamtumEnergy):
+class ElectrostaticEnergy(QuantumEnergy):
     """
     Physical property section describing the electrostatic energy (nuclei + electrons) of a (sub)system.
     """
@@ -413,7 +413,7 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class NuclearRepulsionEnergy(QuamtumEnergy):
+class NuclearRepulsionEnergy(QuantumEnergy):
     """
     Physical property section describing the nuclear-nuclear repulsion energy of a (sub)system.
     """

diff --git a/src/nomad_simulations/properties/forces.py b/src/nomad_simulations/properties/forces.py
@@ -41,105 +41,116 @@
 
 from nomad_simulations.physical_property import PhysicalProperty
 
+####################################################
+# Abstract force classes
+####################################################
 
-################################
-# List of Forces Contributions #
-################################
-
-
-class FreeForce(PhysicalProperty):
+class Force(PhysicalProperty):
     """
-    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.
+    Abstract physical property section describing some energy of a (sub)system.
     """
 
+    type = Quantity(
+        type=MEnum('classical', 'quantum'),
+        description="""
+        """,
+    )
+
     value = Quantity(
         type=np.dtype(np.float64),
-        shape=['n_atoms', 3],
         unit='newton',
         description="""
-        The value of the free force.
+        The value of the force.
         """,
     )
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+######################################################
+# List of general force properties/contributions that
+# can have both classical and quantum interpretations
+######################################################
 
-class ZeroTemperatureForce(PhysicalProperty):
+class TotalForce(Force):
     """
-    Contains the value and information regarding the forces on the atoms
-    corresponding to the minus gradient of energy_T0.
+    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.dtype(np.float64),
-        shape=['n_atoms', 3],
-        unit='newton',
-        description="""
-        The value of the free force.
-        """,
+    contributions = SubSection(
+        sub_section=Force.m_def, repeats=True
     )
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
 
-class RawForce(PhysicalProperty):
-    """ """
+################################
+# List of Forces Contributions #
+################################
 
-    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.
-        """,
-        # ? This is VERY imprecise, is this used regularly?
-    )
+
+class FreeForce(Force):
+    """
+    Physical property section describing...
+
+    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.
+    """
 
     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):
+
+class ZeroTemperatureForce(Force):
     """
-    Section containing contributions to the potential energy from a classical force field.
+    Physical property section describing...
+
+    Contains the value and information regarding the forces on the atoms
+    corresponding to the minus gradient of energy_T0.
     """
 
-    free = SubSection(sub_section=FreeForce.m_def, repeats=False)
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
 
-    zero_temperature_force = SubSection(
-        sub_section=ZeroTemperatureForce.m_def, repeats=False
-    )
 
-    raw = SubSection(sub_section=RawForce.m_def, repeats=False)
+class RawForce(Force):
+    """
+    Physical property section describing...
+
+    Value of the forces acting on the atoms **not including** such as fixed atoms,
+    distances, angles, dihedrals, etc.
+    """
+    # ? This is VERY imprecise, is this used regularly?
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
-        self.name = self.m_def.name
+
+
+# ? 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,
+# )
 
 
 # Old version of the Forces description
@@ -149,28 +160,4 @@ def normalize(self, archive, logger) -> None:
 # 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="""
-        The value of the total force.
-        """,
-    )
-
-    contributions = SubSection(
-        sub_section=ForceContributions.m_def, repeats=False
-    )
-    # ? Do we need to separate classical and quantum contributions here?
-
-    def normalize(self, archive, logger) -> None:
-        super().normalize(archive, logger)