Commit 44e5d29a authored by Alvin Noe Ladines's avatar Alvin Noe Ladines Committed by Markus Scheidgen
Browse files

Implemented new full parsers, minor metainfo updates

parent 72bb10ab
Pipeline #127303 passed with stages
in 51 minutes and 43 seconds
Subproject commit 958d4f2ef91563791ebfe6b329fae5615d992024 Subproject commit 7a57120d6b4845f471577af75ad3e205ee503ea5
Subproject commit 122d8347e79cd4e77adfcc6db4962b10b6075801 Subproject commit eee9bd051c3c52e3560cdb8092f79488dee05009
Subproject commit d9d499b873b1bd1847a13376acc48a928661036a Subproject commit 4050431cce67d80793e548e7f79e44de7e95ecb8
...@@ -310,7 +310,7 @@ class Energy(MSection): ...@@ -310,7 +310,7 @@ class Energy(MSection):
energy calculated with the functional stored in XC_functional. energy calculated with the functional stored in XC_functional.
''') ''')
# TODO Could potential be generalized for other energy types # TODO Remove this should use xc.potential
xc_potential = SubSection( xc_potential = SubSection(
sub_section=EnergyEntry.m_def, sub_section=EnergyEntry.m_def,
description=''' description='''
...@@ -335,6 +335,7 @@ class Energy(MSection): ...@@ -335,6 +335,7 @@ class Energy(MSection):
energy. energy.
''') ''')
# TODO remove this or electrostatic
coulomb = SubSection( coulomb = SubSection(
sub_section=EnergyEntry.m_def, sub_section=EnergyEntry.m_def,
description=''' description='''
...@@ -528,6 +529,38 @@ class Forces(MSection): ...@@ -528,6 +529,38 @@ 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='''
...@@ -1129,6 +1162,7 @@ class Multipoles(MSection): ...@@ -1129,6 +1162,7 @@ class Multipoles(MSection):
higher_order = SubSection(sub_section=MultipolesEntry.m_def, repeats=True) higher_order = SubSection(sub_section=MultipolesEntry.m_def, repeats=True)
# TODO remove this section
class Thermodynamics(MSection): class Thermodynamics(MSection):
''' '''
Section containing results related to a thermodynamics calculation. Section containing results related to a thermodynamics calculation.
...@@ -1564,6 +1598,37 @@ class BaseCalculation(MSection): ...@@ -1564,6 +1598,37 @@ class BaseCalculation(MSection):
contamination in spin-unrestricted calculations. contamination in spin-unrestricted calculations.
''') ''')
pressure = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='pascal',
description='''
Value of the pressure of the system.
''')
temperature = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='kelvin',
description='''
Value of the temperature of the system at which the properties are calculated.
''')
time_physical = Quantity(
type=np.dtype(np.int32),
shape=[],
unit='second',
description='''
The elapsed time with respect to the start of the simulation.
''')
time_step = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
The number of time steps with respect to the start of the simulation.
''')
energy = SubSection(sub_section=Energy.m_def, categories=[FastAccess]) energy = SubSection(sub_section=Energy.m_def, categories=[FastAccess])
forces = SubSection(sub_section=Forces.m_def) forces = SubSection(sub_section=Forces.m_def)
......
...@@ -232,7 +232,7 @@ class MoleculeParameters(MSection): ...@@ -232,7 +232,7 @@ class MoleculeParameters(MSection):
Number of atoms in the molecule. Number of atoms in the molecule.
''') ''')
atoms = SubSection(sub_section=AtomParameters.m_def, repeats=True) atom_parameters = SubSection(sub_section=AtomParameters.m_def, repeats=True)
class GaussianBasisGroup(MSection): class GaussianBasisGroup(MSection):
...@@ -432,8 +432,7 @@ class Interaction(MSection): ...@@ -432,8 +432,7 @@ class Interaction(MSection):
type=str, type=str,
shape=[], shape=[],
description=''' description='''
Denotes the classification of the potential. Could be one of pair, LJ, Morse, EAM, Denotes the classification of the potential.
MEAM.
''') ''')
name = Quantity( name = Quantity(
...@@ -444,16 +443,24 @@ class Interaction(MSection): ...@@ -444,16 +443,24 @@ class Interaction(MSection):
cut-offs, potential versions. cut-offs, potential versions.
''') ''')
n_atoms = Quantity(
type=np.dtype(np.int32),
shape=[],
description='''
Number of atoms included in the interaction
'''
)
atom_labels = Quantity( atom_labels = Quantity(
type=str, type=str,
shape=[2], shape=['n_atoms'],
description=''' description='''
Labels of the atoms described by the interaction. Labels of the atoms described by the interaction.
''') ''')
atom_indices = Quantity( atom_indices = Quantity(
type=np.dtype(np.int32), type=np.dtype(np.int32),
shape=[2], shape=['n_atoms'],
description=''' description='''
Indices of the atoms in the system described by the interaction. Indices of the atoms in the system described by the interaction.
''') ''')
......
...@@ -399,7 +399,7 @@ class Constraint(MSection): ...@@ -399,7 +399,7 @@ class Constraint(MSection):
Number of atoms involved in this constraint. Number of atoms involved in this constraint.
''') ''')
indices = Quantity( atom_indices = Quantity(
type=np.dtype(np.int32), type=np.dtype(np.int32),
shape=['n_constraints', 'n_atoms'], shape=['n_constraints', 'n_atoms'],
description=''' description='''
......
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