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Reorganized in 3 modules
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@JosePizarro3
JosePizarro3 committed Apr 5, 2024
1 parent dea6fa4 commit b11e5af
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Showing 3 changed files with 266 additions and 217 deletions.
221 changes: 4 additions & 217 deletions src/nomad_simulations/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,227 +22,14 @@

from nomad.units import ureg
from nomad.datamodel.data import ArchiveSection
from nomad.metainfo import (
Quantity,
SubSection,
SectionProxy,
Reference,
Section,
Context,
MEnum,
)
from nomad.metainfo.metainfo import DirectQuantity, Dimension
from nomad.metainfo import Quantity, SubSection, MEnum
from nomad.datamodel.metainfo.annotations import ELNAnnotation
from nomad.datamodel.metainfo.basesections import Entity

from .model_system import ModelSystem
from .numerical_settings import SelfConsistency
from .physical_property import PhysicalProperty


class Variables(ArchiveSection):
""" """

name = Quantity(type=str)
n_bins = Quantity(type=int)
bins = Quantity(type=np.float64, shape=['n_bins'])
# bins_error = Quantity()

def normalize(self, archive, logger) -> None:
super().normalize(archive, logger)


class Temperatures(Variables):
def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
super().__init__(m_def, m_context, **kwargs)
self.name = self.m_def.name


class Energies(Variables):
def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
super().__init__(m_def, m_context, **kwargs)
self.name = self.m_def.name


class PhysicalProperty(ArchiveSection):
""" """

source = Quantity(
type=MEnum('simulation', 'measurement', 'analysis'),
default='simulation',
description="""
Source of the physical property. Example: an `ElectronicBandGap` can be obtained from a `'simulation'`
or in an `'measurement'`.
""",
)

type = Quantity(
type=str,
description="""
Type categorization of the physical property. Example: an `ElectronicBandGap` can be `'direct'`
or `'indirect'`.
""",
)

label = Quantity(
type=str,
description="""
Label for additional classification of the physical property. Example: an `ElectronicBandGap`
can be labeled as `'DFT'` or `'GW'` depending on the methodology used to calculate it.
""",
)

shape = DirectQuantity(
type=Dimension,
shape=['0..*'],
default=[],
name='shape',
description="""
Shape of the physical property. This quantity is related with the order of the tensor which
describes the physical property:
- scalars (tensor order 0) have `shape=[]` (`len(shape) = 0`),
- vectors (tensor order 1) have `shape=[a]` (`len(shape) = 1`),
- matrices (tensor order 2), have `shape=[a, b]` (`len(shape) = 2`),
- etc.
""",
)

variables = SubSection(
type=Variables.m_def,
description="""
Variables over which the physical property varies. These are defined as binned, i.e., discretized
values by `n_bins` and `bins`. The `variables` are used to calculate the `variables_shape` of the physical property.
""",
repeats=True,
)

# ! this is not working for now, because I want to m_set the values of `n_bins` and `bins` like `MSection` has implemented
# variables = Quantity(
# type=Variables,
# shape=['*'],
# description="""
# Variables over which the physical property varies. These are defined as binned, i.e., discretized
# values by `n_bins` and `bins`. The `variables` are used to calculate the `variables_shape` of the physical property.
# """,
# )

# overwrite this with the specific description of the physical property
value = Quantity()
# value_unit = Quantity(type=str)

entity_ref = Quantity(
type=Entity,
description="""
Reference to the entity that the physical property refers to.
""",
)

outputs_ref = Quantity(
type=Reference(SectionProxy('PhysicalProperty')),
description="""
Reference to the `PhysicalProperty` section from which the physical property was derived. If `outputs_ref`
is populated, the quantity `is_derived` is set to True via normalization.
""",
)

is_derived = Quantity(
type=bool,
default=False,
description="""
Flag indicating whether the physical property is derived from other physical properties. We make
the distinction between directly parsed and derived physical properties:
- Directly parsed: the physical property is directly parsed from the simulation output files.
- Derived: the physical property is derived from other physical properties. No extra numerical settings
are required to calculate the physical property.
""",
)

@property
def get_variables_shape(self) -> list:
"""
Shape of the variables over which the physical property varies. This is extracted from
`Variables.n_bins` and appended in a list.
Example, a physical property which varies with `Temperature` and `ElectricField` will
return `variables_shape = [n_temperatures, n_electric_fields]`.
Returns:
(list): The shape of the variables over which the physical property varies.
"""
return [v.n_bins for v in self.variables]

@property
def get_full_shape(self) -> list:
"""
Full shape of the physical property. This quantity is calculated as:
`full_shape = variables_shape + shape`
where `shape` is passed as an attribute of the `PhysicalProperty` and is related with the order of
the tensor of `value`, and `variables_shape` is obtained from `get_variables_shape` and is
related with the shapes of the `variables` over which the physical property varies.
Example: a physical property which is a 3D vector and varies with `variables=[Temperature, ElectricField]`
will have `shape = [3]`, `variables_shape=[n_temperatures, n_electric_fields]`, and thus
`full_shape=[n_temperatures, n_electric_fields, 3]`.
Returns:
(list): The full shape of the physical property.
"""
return self.get_variables_shape + self.shape

def __init__(self, m_def: Section = None, m_context: Context = None, **kwargs):
super().__init__(m_def, m_context, **kwargs)

# initialize a `_new_value` quantity copying the main attrs from the `_value` quantity (`type`, `unit`,
# `description`); this will then be used to setattr the `value` quantity to the `_new_value` one with the
# correct `shape=_full_shape`
for quant in self.m_def.quantities:
if quant.name == 'value':
self._new_value = Quantity(
type=quant.type,
unit=quant.unit, # ? this can be moved to __setattr__
description=quant.description,
)
break

def __setattr__(self, name: str, val: Any) -> None:
# For the special case of `value`, its `shape` needs to be defined from `_full_shape`
if name == 'value':
# * This setattr logic for `value` only works if `variables` and `shape` have been stored BEFORE the `value` is set
_full_shape = self.get_full_shape

# non-scalar or scalar `val`
try:
value_shape = list(val.shape)
except AttributeError:
value_shape = []

if value_shape != _full_shape:
raise ValueError(
f'The shape of the stored `value` {value_shape} does not match the full shape {_full_shape} extracted from the variables `n_bins` and the `shape` defined in `PhysicalProperty`.'
)
self._new_value.shape = _full_shape
self._new_value = val.magnitude * val.u
return super().__setattr__(name, self._new_value)
return super().__setattr__(name, val)

def _is_derived(self) -> bool:
"""
Resolves if the output property is derived or not.
Args:
outputs_ref (_type_): The reference to the `Outputs` section from which the output property was derived.
Returns:
bool: The flag indicating whether the output property is derived or not.
"""
if self.outputs_ref is not None:
return True
return False

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()
from .variables import Variables, Temperatures # ? delete these imports


class ElectronicBandGap(PhysicalProperty):
Expand Down Expand Up @@ -352,7 +139,7 @@ def normalize(self, archive, logger) -> None:
n_bins = 3
temperature = Temperatures(n_bins=n_bins, bins=np.linspace(0, 100, n_bins))
band_gap.variables.append(temperature)
n_bins = 6
n_bins = 2
custom_bins = Variables(n_bins=n_bins, bins=np.linspace(0, 100, n_bins))
band_gap.variables.append(custom_bins)
# band_gap.value_unit = 'joule'
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