Commit 67af7ac4 authored by Alvin Noe Ladines's avatar Alvin Noe Ladines
Browse files

Minor metainfo refactor, new parsers

parent 81d03231
Pipeline #128934 failed with stages
in 10 minutes and 53 seconds
Subproject commit ef6209c60f3a4a92b5411f9bdef1dd7a326ed32c Subproject commit 725ed6ca3b65fe44e7ab9023ded2db5f84a6a880
Subproject commit eee9bd051c3c52e3560cdb8092f79488dee05009 Subproject commit d1eaaf31da27402c33d90559d3f21af7ee9a2294
Subproject commit 4050431cce67d80793e548e7f79e44de7e95ecb8 Subproject commit e1dc7c53061d5cf282e3784578d43c38bc972c82
...@@ -126,6 +126,7 @@ class AtomicValues(MSection): ...@@ -126,6 +126,7 @@ class AtomicValues(MSection):
m_def = Section(validate=False) m_def = Section(validate=False)
# TODO rename this to spin_channel
spin = Quantity( spin = Quantity(
type=np.dtype(np.int32), type=np.dtype(np.int32),
shape=[], shape=[],
...@@ -210,6 +211,7 @@ class EnergyEntry(Atomic): ...@@ -210,6 +211,7 @@ class EnergyEntry(Atomic):
cell. cell.
''') ''')
# TODO rename this to value_atomic
values_per_atom = Quantity( values_per_atom = Quantity(
type=np.dtype(np.float64), type=np.dtype(np.float64),
shape=['n_atoms'], shape=['n_atoms'],
...@@ -409,6 +411,38 @@ class Energy(MSection): ...@@ -409,6 +411,38 @@ class Energy(MSection):
''', ''',
repeats=True) repeats=True)
enthalpy = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
''')
entropy = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule / kelvin',
description='''
Value of the entropy.
''')
chemical_potential = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the chemical potential.
''')
internal = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the internal energy.
''')
# TODO remove this should be be entropy.correction # TODO remove this should be be entropy.correction
correction_entropy = SubSection( correction_entropy = SubSection(
sub_section=EnergyEntry.m_def, sub_section=EnergyEntry.m_def,
...@@ -529,38 +563,6 @@ class Forces(MSection): ...@@ -529,38 +563,6 @@ class Forces(MSection):
corresponding to the minus gradient of energy_T0. corresponding to the minus gradient of energy_T0.
''') ''')
enthalpy = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the calculated enthalpy per cell i.e. energy_total + pressure * volume.
''')
entropy = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule / kelvin',
description='''
Value of the entropy.
''')
chemical_potential = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the chemical potential.
''')
internal = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the internal energy.
''')
contributions = SubSection( contributions = SubSection(
sub_section=ForcesEntry.m_def, sub_section=ForcesEntry.m_def,
description=''' description='''
...@@ -646,6 +648,20 @@ class ChargesValue(AtomicValues): ...@@ -646,6 +648,20 @@ class ChargesValue(AtomicValues):
Value of the charge projected on atom and orbital. Value of the charge projected on atom and orbital.
''') ''')
n_electrons = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Value of the number of electrons projected on atom and orbital.
''')
spin_z = Quantity(
type=np.dtype(np.float64),
shape=[],
description='''
Value of the azimuthal spin projected on atom and orbital.
''')
class Charges(Atomic): class Charges(Atomic):
''' '''
...@@ -670,6 +686,15 @@ class Charges(Atomic): ...@@ -670,6 +686,15 @@ class Charges(Atomic):
Value of the atomic charges calculated through analysis_method. Value of the atomic charges calculated through analysis_method.
''') ''')
n_electrons = Quantity(
type=np.dtype(np.float64),
shape=['n_atoms'],
description='''
Value of the number of electrons on the atoms.
''')
# TODO should this be on a separate section magnetic_moments or charges should be
# renamed population
spins = Quantity( spins = Quantity(
type=np.dtype(np.float64), type=np.dtype(np.float64),
shape=['n_atoms'], shape=['n_atoms'],
...@@ -1428,7 +1453,7 @@ class ExcitedStates(MSection): ...@@ -1428,7 +1453,7 @@ class ExcitedStates(MSection):
''') ''')
class VibrationsValues(MSection): class VibrationalFrequenciesValues(MSection):
''' '''
Section describing a vibrational spectrum. Section describing a vibrational spectrum.
''' '''
...@@ -1472,7 +1497,7 @@ class VibrationsValues(MSection): ...@@ -1472,7 +1497,7 @@ class VibrationsValues(MSection):
''') ''')
class Vibrations(MSection): class VibrationalFrequencies(MSection):
''' '''
Section containing results related to vibrational frequencies. Section containing results related to vibrational frequencies.
''' '''
...@@ -1491,12 +1516,14 @@ class Vibrations(MSection): ...@@ -1491,12 +1516,14 @@ class Vibrations(MSection):
shape=['n_frequencies'], shape=['n_frequencies'],
unit='1 / meter', unit='1 / meter',
description=''' description='''
Values of vibration Frequenices (cm-1) Values of vibrational frequencies (m-1)
''') ''')
raman = SubSection(sub_section=VibrationsValues.m_def, repeats=False) # TODO add normal modes
raman = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
infrared = SubSection(sub_section=VibrationsValues.m_def, repeats=False) infrared = SubSection(sub_section=VibrationalFrequenciesValues.m_def, repeats=False)
class BaseCalculation(MSection): class BaseCalculation(MSection):
...@@ -1649,7 +1676,7 @@ class BaseCalculation(MSection): ...@@ -1649,7 +1676,7 @@ class BaseCalculation(MSection):
excited_states = SubSection(sub_section=ExcitedStates.m_def, repeats=True) excited_states = SubSection(sub_section=ExcitedStates.m_def, repeats=True)
vibrational_frequencies = SubSection(sub_section=Vibrations.m_def, repeats=True) vibrational_frequencies = SubSection(sub_section=VibrationalFrequencies.m_def, repeats=True)
potential = SubSection(sub_section=Potential.m_def, repeats=True) potential = SubSection(sub_section=Potential.m_def, repeats=True)
......
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