added force contributions, fixed energies, import changes

Author: jrudz

src/nomad_simulations/outputs.py

@@ -41,7 +41,8 @@
     AbsorptionSpectrum,
     XASSpectrum,
     Permittivity,
-    TotalEnergy
+    TotalEnergy,
+    TotalForce,
 )
 
 
@@ -112,7 +113,9 @@ class Outputs(ArchiveSection):
 
     xas_spectra = SubSection(sub_section=XASSpectrum.m_def, repeats=True)
 
-    total_energy = SubSection(SubSection=TotalEnergy.m_def, repeats=True)
+    total_energy = SubSection(sub_section=TotalEnergy.m_def, repeats=True)
+
+    total_force = SubSection(sub_section=TotalForce.m_def, repeats=True)
 
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
     # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
@@ -296,6 +299,7 @@ def normalize(self, archive, logger) -> None:
                     logger=logger,
                 )
 
+
 class WorkflowOutputs(Outputs):
     """
     This section contains output properties that depend on a single system, but were
@@ -320,6 +324,7 @@ class WorkflowOutputs(Outputs):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class TrajectoryOutputs(WorkflowOutputs):
     """
     This section contains output properties that depend on a single system, but were
@@ -328,6 +333,7 @@ class TrajectoryOutputs(WorkflowOutputs):
 
     time = Quantity(
         type=np.float64,
+        unit='ps',
         description="""
         The elapsed simulated physical time since the start of the trajectory.
         """,

src/nomad_simulations/physical_property.py

@@ -320,4 +320,4 @@ def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
         # Resolve if the physical property `is_derived` or not from another physical property.
-        self.is_derived = self._is_derived()
+        self.is_derived = self._is_derived()

src/nomad_simulations/properties/__init__.py

@@ -23,6 +23,7 @@
     ClassicalEnergyContributions,
     QuantumEnergyContributions,
 )
+from .forces import TotalForce, ForceContributions
 from .band_gap import ElectronicBandGap
 from .spectral_profile import (
     SpectralProfile,

src/nomad_simulations/properties/energies.py

@@ -19,9 +19,11 @@
 import numpy as np
 
 from nomad.metainfo import Quantity, Section, Context, SubSection, MEnum
+from nomad.datamodel.data import ArchiveSection
 
 from nomad_simulations.physical_property import PhysicalProperty
 
+
 class FermiLevel(PhysicalProperty):
     """
     Energy required to add or extract a charge from a material at zero temperature. It can be also defined as the chemical potential at zero temperature.
@@ -82,6 +84,7 @@ def normalize(self, archive, logger) -> None:
 # List of classical energy contribuions
 ####################################################
 
+
 class PotentialEnergy(PhysicalProperty):
     """
     Section containing the potential energy of a (sub)system.
@@ -98,6 +101,7 @@ class PotentialEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class KineticEnergy(PhysicalProperty):
     """
     Section containing the kinetic energy of a (sub)system.
@@ -152,6 +156,7 @@ class VDWEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ElectrostaticEnergy(PhysicalProperty):
     """
     Section containing all electrostatic contributions to the potential energy of a (sub)system.
@@ -168,6 +173,7 @@ class ElectrostaticEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ElectrostaticShortRangeEnergy(PhysicalProperty):
     """
     Section containing short-range electrostatic contributions to the potential energy of a (sub)system.
@@ -184,6 +190,7 @@ class ElectrostaticShortRangeEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ElectrostaticLongRangeEnergy(PhysicalProperty):
     """
     Section containing long-range electrostatic contributions to the potential energy of a (sub)system.
@@ -200,6 +207,7 @@ class ElectrostaticLongRangeEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class BondedEnergy(PhysicalProperty):
     """
     Section containing all bonded (i.e., intramolecular) contributions to the potential energy of a (sub)system.
@@ -216,6 +224,7 @@ class BondedEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class BondEnergy(PhysicalProperty):
     """
     Section containing contributions to the potential energy from bond interactions of a (sub)system.
@@ -232,6 +241,7 @@ class BondEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class AngleEnergy(PhysicalProperty):
     """
     Section containing contributions to the potential energy from angle interactions of a (sub)system.
@@ -248,6 +258,7 @@ class AngleEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class DihedralEnergy(PhysicalProperty):
     """
     Section containing contributions to the potential energy from dihedral interactions of a (sub)system.
@@ -264,6 +275,7 @@ class DihedralEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ImproperDihedralEnergy(PhysicalProperty):
     """
     Section containing contributions to the potential energy from improper dihedral interactions of a (sub)system.
@@ -280,6 +292,7 @@ class ImproperDihedralEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ExternalEnergy(PhysicalProperty):
     """
     Section containing contributions to the potential energy from external interactions of a (sub)system.
@@ -296,6 +309,7 @@ class ExternalEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ClassicalEnergyContributions(ArchiveSection):
     """
     Section containing contributions to the potential energy from a classical force field.
@@ -309,9 +323,13 @@ class ClassicalEnergyContributions(ArchiveSection):
 
     electrostatic = SubSection(sub_section=ElectrostaticEnergy.m_def, repeats=False)
 
-    electrostatic_short_range = SubSection(sub_section=ElectrostaticShortRangeEnergy.m_def, repeats=False)
+    electrostatic_short_range = SubSection(
+        sub_section=ElectrostaticShortRangeEnergy.m_def, repeats=False
+    )
 
-    electrostatic_long_range = SubSection(sub_section=ElectrostaticLongRangeEnergy.m_def, repeats=False)
+    electrostatic_long_range = SubSection(
+        sub_section=ElectrostaticLongRangeEnergy.m_def, repeats=False
+    )
 
     bonded = SubSection(sub_section=BondedEnergy.m_def, repeats=False)
 
@@ -321,7 +339,9 @@ class ClassicalEnergyContributions(ArchiveSection):
 
     dihedral = SubSection(sub_section=DihedralEnergy.m_def, repeats=False)
 
-    improper_dihedral = SubSection(sub_section=ImproperDihedralEnergy.m_def, repeats=False)
+    improper_dihedral = SubSection(
+        sub_section=ImproperDihedralEnergy.m_def, repeats=False
+    )
 
     external = SubSection(sub_section=ExternalEnergy.m_def, repeats=False)
 
@@ -330,10 +350,12 @@ def normalize(self, archive, logger) -> None:
         # Set the name of the section
         self.name = self.m_def.name
 
+
 ######################################
 # List of quantum energy contributions
 ######################################
 
+
 class ElectronicEnergy(PhysicalProperty):
     """
     Section containing the electronic energy of a (sub)system.
@@ -347,12 +369,11 @@ class ElectronicEnergy(PhysicalProperty):
         """,
     )
 
-    contributions = SubSection(sub_section=EnergyContributions.m_def, repeats=True)
-
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
         allowed_contributions = ['PotKin']
 
+
 class ElectronicKineticEnergy(PhysicalProperty):
     """
     Section containing the electronic kinetic energy of a (sub)system.
@@ -369,11 +390,13 @@ class ElectronicKineticEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class XCEnergy(PhysicalProperty):
     """
     Section containing the exchange-correlation (XC) energy of a (sub)system,
     calculated using the functional stored in XC_functional.
     """
+
     # ! Someone check this description!
     # ? Do we really want to specify the method here? This can't be user-defined?
 
@@ -388,6 +411,7 @@ class XCEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class XCPotentialEnergy(PhysicalProperty):
     """
     Section containing the potential energy contribution to the exchange-correlation (XC) energy,
@@ -396,6 +420,7 @@ class XCPotentialEnergy(PhysicalProperty):
         of XC that is in the sum of the eigenvalues. Value associated with the
         configuration, should be the most converged value.          |
     """
+
     # ! Someone check this description!
     # ? Do we really want to specify the method here? This can't be user-defined?
 
@@ -410,12 +435,14 @@ class XCPotentialEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 # ? XCCorrelationEnergy?
 class CorrelationEnergy(PhysicalProperty):
     """
     Section containing the correlation energy of a (sub)system,
     calculated using the method described in XC_functional.
     """
+
     # ! Someone check this description!
     # ? Do we really want to specify the method here? This can't be user-defined?
 
@@ -430,12 +457,14 @@ class CorrelationEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 # ? XCExchangeEnergy?
 class ExchangeEnergy(PhysicalProperty):
     """
     Section containing the exchange energy of a (sub)system,
     calculated using the method described in XC_functional.
     """
+
     # ! Someone check this description!
     # ? Do we really want to specify the method here? This can't be user-defined?
 
@@ -468,11 +497,13 @@ class ZeroTemperatureEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ZeroPointEnergy(PhysicalProperty):
     """
     Section containing the zero-point vibrational energy of a (sub)system,
     calculated using the method described in zero_point_method.
     """
+
     # ! Someone check this description!
     # ? Do we really want to specify the method here? This can't be user-defined?
 
@@ -487,6 +518,7 @@ class ZeroPointEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class ElectrostaticEnergy(PhysicalProperty):
     """
     Section containing the electrostatic energy (nuclei + electrons) of a (sub)system.
@@ -503,6 +535,7 @@ class ElectrostaticEnergy(PhysicalProperty):
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
 
+
 class NuclearRepulsionEnergy(PhysicalProperty):
     """
     Section containing the nuclear-nuclear repulsion energy of a (sub)system.
@@ -524,11 +557,14 @@ class QuantumEnergyContributions(ArchiveSection):
     """
     Section containing contributions to the potential energy from a DFT calculation.
     """
-...
+
+    ...
 
     electronic = SubSection(sub_section=ElectronicEnergy.m_def, repeats=False)
 
-    electronic_kinetic = SubSection(sub_section=ElectronicKineticEnergy.m_def, repeats=False)
+    electronic_kinetic = SubSection(
+        sub_section=ElectronicKineticEnergy.m_def, repeats=False
+    )
 
     xc = SubSection(sub_section=XCEnergy.m_def, repeats=False)
 
@@ -538,18 +574,24 @@ class QuantumEnergyContributions(ArchiveSection):
 
     exchange = SubSection(sub_section=ExchangeEnergy.m_def, repeats=False)
 
-    zero_temperature = SubSection(sub_section=ZeroTemperatureEnergy.m_def, repeats=False)
+    zero_temperature = SubSection(
+        sub_section=ZeroTemperatureEnergy.m_def, repeats=False
+    )
 
     zero_point = SubSection(sub_section=ZeroPointEnergy.m_def, repeats=False)
 
     electrostatic = SubSection(sub_section=ElectrostaticEnergy.m_def, repeats=False)
 
-    nuclear_repulsion = SubSection(sub_section=NuclearRepulsionEnergy.m_def, repeats=False)
+    nuclear_repulsion = SubSection(
+        sub_section=NuclearRepulsionEnergy.m_def, repeats=False
+    )
+
 
 ##########################
 # Other / General energies
 ##########################
 
+
 class TotalEnergy(PhysicalProperty):
     """
     Section containing the total energy of a (sub)system.
@@ -564,12 +606,17 @@ class TotalEnergy(PhysicalProperty):
     )
     # ? Do we need these descriptions under value? It ends up simply duplicating the section info to some extent.
 
-    classical_contributions = SubSection(sub_section=ClassicalEnergyContributions.m_def, repeats=False)
+    classical_contributions = SubSection(
+        sub_section=ClassicalEnergyContributions.m_def, repeats=False
+    )
 
-    quantum_contributions = SubSection(sub_section=QuantumEnergyContributions.m_def, repeats=False)
+    quantum_contributions = SubSection(
+        sub_section=QuantumEnergyContributions.m_def, repeats=False
+    )
 
     def normalize(self, archive, logger) -> None:
         super().normalize(archive, logger)
+        #? Should we set total energy value as sum of all contributions if not set explicitly?
 
     # madelung = SubSection(
     #     sub_section=EnergyEntry.m_def,
@@ -709,7 +756,6 @@ def normalize(self, archive, logger) -> None:
     #     """,
     # )
 
-
     # # TODO this should be removed and replaced by correction in EnergyEntry
     # current = SubSection(
     #     sub_section=EnergyEntry.m_def,
@@ -723,8 +769,6 @@ def normalize(self, archive, logger) -> None:
     # )
 
 
-
-
 # # ? Do we want to allow this?
 # class EnergyCustom(PhysicalProperty):
 #     """