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created AtomicProperty
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jrudz committed Apr 2, 2024
1 parent 32ef9a3 commit 93ceaa0
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201 changes: 50 additions & 151 deletions src/nomad_simulations/outputs_JFR_temp.py
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from nomad.metainfo.metainfo import DirectQuantity, Dimension
from nomad.datamodel.metainfo.annotations import ELNAnnotation

from outputs import Outputs
from property import BaseProperty
from .outputs import Outputs
from .property import BaseProperty
from .atoms_state import AtomsState



#
# 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.datamodel.data import ArchiveSection
from nomad.datamodel.metainfo.common import (
FastAccess,
PropertySection,
Expand All @@ -87,183 +67,105 @@
SubSection,
)

from .method import HoppingMatrix, Method
from .system import AtomsGroup, System

m_package = Package()



class EnergyValue(MCategory):
"""
This metadata stores an energy value.
"""

m_def = Category()


class EnergyTypeReference(MCategory):
"""
This metadata stores an energy used as reference point.
"""

m_def = Category(categories=[EnergyValue])


class ErrorEstimateContribution(MCategory):
"""
An estimate of a partial quantity contributing to the error for a given quantity.
"""

m_def = Category()
from .model_system import ModelSystem


class Atomic(MSection):
class AtomicProperty(BaseProperty):
"""
Generic section containing the values and information reqarding an atomic quantity
such as charges, forces, multipoles.
"""

m_def = Section(validate=False)

kind = Quantity(
type=str,
shape=[],
description="""
Kind of the quantity.
""",
)

n_orbitals = Quantity(
type=np.int32,
shape=[],
description="""
Number of orbitals used in the projection.
""",
)
# ? Is "the projection" general/clear?

# TODO we should make clear in these descriptions that it is preferred to reference the relevant sub-system if existing,
# TODO otherwise these quantities can be populated "by hand"
n_atoms = Quantity(
type=np.int32,
shape=[],
description="""
Number of atoms.
Number of atoms used to determine/calculate the property.
""",
)

n_spin_channels = Quantity(
type=np.int32,
shape=[],
description="""
Number of spin channels.
""",
)


class AtomicValues(ArchiveSection):
"""
Generic section containing information regarding the values of an atomic quantity.
"""

m_def = Section(validate=False)

# TODO rename this to spin_channel
spin = Quantity(
type=np.dtype(np.int32),
shape=[],
description="""
Spin channel corresponding to the atomic quantity.
""",
)

atom_label = Quantity(
atom_labels = Quantity(
type=str,
shape=[],
description="""
Label of the atomic species corresponding to the atomic quantity.
Labels of the atomic species corresponding to the atomic quantity.
""",
)

atom_index = Quantity(
atom_indices = Quantity(
type=np.dtype(np.int32),
shape=[],
description="""
Index of the atomic species corresponding to the atomic quantity.
""",
)

m_kind = Quantity(
type=str,
n_spin_channels = Quantity(
type=np.int32,
shape=[],
description="""
String describing what the integer numbers of $m$ lm mean used in orbital
projections. The allowed values are listed in the [m_kind wiki page]
(https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
Number of spin channels.
""",
)

lm = Quantity(
spin_channels = Quantity(
type=np.dtype(np.int32),
shape=[2],
description="""
Tuples of $l$ and $m$ values for which the atomic quantity are given. For
the quantum number $l$ the conventional meaning of azimuthal quantum number is
always adopted. For the integer number $m$, besides the conventional use as
magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
different conventions is accepted (see the [m_kind wiki
page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
The adopted convention is specified by m_kind.
""",
)

orbital = Quantity(
type=str,
shape=[],
description="""
String representation of the of the atomic orbital.
Spin channels corresponding to the atomic quantity.
""",
)


class AtomicGroup(MSection):
"""
Generic section containing the values and information reqarding a molecular or sub-molecular
quantity that is a function of an atomic group such as radius of gyration...
"""

m_def = Section(validate=False)

kind = Quantity(
type=str,
shape=[],
atoms_state_ref = Quantity(
type=AtomsState,
description="""
Kind of the quantity.
Reference to the AtomsState section for the atoms involved in this property.
""",
)

# ? below deprecated by atoms_state?
# m_kind = Quantity(
# type=str,
# shape=[],
# description="""
# String describing what the integer numbers of $m$ lm mean used in orbital
# projections. The allowed values are listed in the [m_kind wiki page]
# (https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
# """,
# )

class AtomicGroupValues(MSection):
"""
Generic section containing information regarding the values of a trajectory property.
"""

m_def = Section(validate=False)

label = Quantity(
type=str,
shape=[],
description="""
Describes the atoms or molecule types involved in determining the property.
""",
)

atomsgroup_ref = Quantity(
type=Reference(AtomsGroup.m_def),
shape=[1],
description="""
References to the atoms_group section containing the molecule for which Rg was calculated.
""",
)
# lm = Quantity(
# type=np.dtype(np.int32),
# shape=[2],
# description="""
# Tuples of $l$ and $m$ values for which the atomic quantity are given. For
# the quantum number $l$ the conventional meaning of azimuthal quantum number is
# always adopted. For the integer number $m$, besides the conventional use as
# magnetic quantum number ($l+1$ integer values from $-l$ to $l$), a set of
# different conventions is accepted (see the [m_kind wiki
# page](https://gitlab.rzg.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/m-kind).
# The adopted convention is specified by m_kind.
# """,
# )

# orbital = Quantity(
# type=str,
# shape=[],
# description="""
# String representation of the of the atomic orbital.
# """,
# )

class EnergyEntry(Atomic):
"""
Expand Down Expand Up @@ -1543,6 +1445,3 @@ class Calculation(BaseCalculation):
)

scf_iteration = SubSection(sub_section=ScfIteration.m_def, repeats=True)


m_package.__init_metainfo__()
16 changes: 12 additions & 4 deletions src/nomad_simulations/property.py
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Expand Up @@ -39,11 +39,12 @@

from nomad.units import ureg
from nomad.datamodel.data import ArchiveSection
from nomad.metainfo import Quantity, SubSection, SectionProxy, MEnum
from nomad.metainfo import Quantity, SubSection, Reference
from nomad.metainfo.metainfo import DirectQuantity, Dimension
from nomad.datamodel.metainfo.annotations import ELNAnnotation

from outputs import Outputs
from .model_system import ModelSystem
from .outputs import Outputs

class BaseErrors(ArchiveSection):
"""
Expand Down Expand Up @@ -108,8 +109,7 @@ def __init__(self, *args, **kwargs):
type = Quantity(
type=str,
description="""
Categorization of the property. Previously used to distinguish "molecular" vs. "atomic" properties.
But could have a variety of uses depending on the context.
Categorization of the property.
""",
a_eln=ELNAnnotation(component='StringEditQuantity'),
)
Expand Down Expand Up @@ -191,6 +191,14 @@ def __init__(self, *args, **kwargs):
""",
)

system_ref = Quantity(
type=Reference(ModelSystem.m_def),
shape=[1],
description="""
References to the (sub)system section containing the atoms relevant for this property.
""",
)

errors = SubSection(sub_section=BaseErrors.m_def, repeats=True)

def normalize(self, archive, logger) -> None:
Expand Down

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