47 add thermodynamics output

src/nomad_simulations/thermodynamics.py

@@ -0,0 +1,238 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+from nomad.metainfo import Quantity, SubSection, MEnum
+from .physical_property import PhysicalProperty
+
+class Enthalpy(PhysicalProperty):
+    """
+    Section containing the enthalpy (i.e. energy_total + pressure * volume.) of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        Value of the enthalpy.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Entropy(PhysicalProperty):
+    """
+    Section containing the entropy of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule / kelvin',
+        description="""
+        Value of the entropy.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class ChemicalPotential(PhysicalProperty):
+    """
+    Section containing the chemical potential of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        Value of the chemical potential.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Pressure(PhysicalProperty):
+    """
+    Section containing the pressure of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='pascal',
+        description="""
+        Value of the pressure.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Virial(PhysicalProperty):
+    """
+    Section containing the virial (cross product between positions and forces) of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule',
+        description="""
+        Value of the pressure.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Temperature(PhysicalProperty):
+    """
+    Section containing the temperature of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='kelvin',
+        description="""
+        Value of the pressure.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Volume(PhysicalProperty):
+    """
+    Section containing the volume of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='m ** 3',
+        description="""
+        Value of the volume.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+class Density(PhysicalProperty):
+    """
+    Section containing the density of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='kg / m ** 3',
+        description="""
+        Value of the density.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+# ? Does this go here or in energies?
+# ? Naming specific to Potential Energy?
+class Hessian(PhysicalProperty):
+    """
+    Section containing the Hessian matrix, i.e., 2nd derivatives with respect to geometric (typically particle) displacements,
+    of the potential energy of a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule / m ** 2',
+        description="""
+        Value of the Hessian.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+class HeatCapacityCV(PhysicalProperty):
+    """
+    Section containing the heat capacity at constant volume for a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule / kelvin',
+        description="""
+        Value of the heat capacity.
+        """,
+    )
+
+class HeatCapacityCP(PhysicalProperty):
+    """
+    Section containing the heat capacity at constant volume for a (sub)system.
+    """
+
+    value = Quantity(
+        type=np.float64,
+        unit='joule / kelvin',
+        description="""
+        Value of the heat capacity.
+        """,
+    )
+
+    def normalize(self, archive, logger) -> None:
+        super().normalize(archive, logger)
+
+
+    # ? Is this ever used?
+    # internal_energy = Quantity(
+    #     type=np.dtype(np.float64),
+    #     shape=[],
+    #     unit='joule',
+    #     description="""
+    #     Value of the internal energy.
+    #     """,
+    # )
+
+    # vibrational_free_energy_at_constant_volume = Quantity(
+    #     type=np.dtype(np.float64),
+    #     shape=[],
+    #     unit='joule',
+    #     description="""
+    #     Value of the vibrational free energy per cell unit at constant volume.
+    #     """,
+    # )
+
+