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):
m_def = Section(validate=False)
# TODO rename this to spin_channel
spin = Quantity(
type=np.dtype(np.int32),
shape=[],
......@@ -210,6 +211,7 @@ class EnergyEntry(Atomic):
cell.
''')
# TODO rename this to value_atomic
values_per_atom = Quantity(
type=np.dtype(np.float64),
shape=['n_atoms'],
......@@ -409,6 +411,38 @@ class Energy(MSection):
''',
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
correction_entropy = SubSection(
sub_section=EnergyEntry.m_def,
......@@ -529,38 +563,6 @@ class Forces(MSection):
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(
sub_section=ForcesEntry.m_def,
description='''
......@@ -646,6 +648,20 @@ class ChargesValue(AtomicValues):
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):
'''
......@@ -670,6 +686,15 @@ class Charges(Atomic):
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(
type=np.dtype(np.float64),
shape=['n_atoms'],
......@@ -1428,7 +1453,7 @@ class ExcitedStates(MSection):
''')
class VibrationsValues(MSection):
class VibrationalFrequenciesValues(MSection):
'''
Section describing a vibrational spectrum.
'''
......@@ -1472,7 +1497,7 @@ class VibrationsValues(MSection):
''')
class Vibrations(MSection):
class VibrationalFrequencies(MSection):
'''
Section containing results related to vibrational frequencies.
'''
......@@ -1491,12 +1516,14 @@ class Vibrations(MSection):
shape=['n_frequencies'],
unit='1 / meter',
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):
......@@ -1649,7 +1676,7 @@ class BaseCalculation(MSection):
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)
......
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