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Add module for material_system and classes for Solid Solution
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‎transmission/transmission_plugin/uv_vis_nir_transmission_plugin/src/uv_vis_nir_transmission/__init__.py‎

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from .schema import *
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from .schema import *
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from .material_systems import *

‎transmission/transmission_plugin/uv_vis_nir_transmission_plugin/src/uv_vis_nir_transmission/material_systems.py‎

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"""
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Module containing NOMAD classes for material systems used in UV/Vis/NIR Transmission.
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"""
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import numpy as np
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from ase.data import chemical_symbols
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from nomad.datamodel.metainfo.basesections import (
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CompositeSystem,
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PubChemPureSubstanceSection,
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PureSubstance,
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SystemComponent,
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EntryData,
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)
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from nomad.metainfo import (
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Quantity,
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SubSection,
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MEnum,
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Section,
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)
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from nomad.datamodel.data import (
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ArchiveSection,
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)
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from nomad.datamodel.metainfo.annotations import (
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ELNAnnotation,
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SectionProperties,
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Filter,
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)
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class CrystalProperties(ArchiveSection):
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pass
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class CrystallinePureSubstance(PureSubstance, EntryData):
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m_def = Section(
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description='A pure substance component having a crystalline structure.',
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a_eln=ELNAnnotation(
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properties=SectionProperties(
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order=[
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'name',
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'substance_name',
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'molecular_formula',
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]
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)
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),
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)
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molecular_formula = Quantity(
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type=str,
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description='Molecular formula of the component.',
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a_eln={'component': 'StringEditQuantity'},
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)
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crystal_properties = SubSection(
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section_def=CrystalProperties,
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description='Properties of the crystalline structure.',
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)
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def normalize(self, archive, logger: 'BoundLogger') -> None:
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# make PubChem API calls when required
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if self.pure_substance is None or self.pure_substance.iupac_name is None:
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pure_substance = PubChemPureSubstanceSection()
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if self.molecular_formula is not None:
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pure_substance.molecular_formula = self.molecular_formula
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pure_substance.normalize(archive, logger)
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if pure_substance.iupac_name is not None:
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# material was found in PubChem database
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self.pure_substance = pure_substance
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self.molecular_formula = pure_substance.molecular_formula
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super().normalize(archive, logger)
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class HostComponent(SystemComponent):
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m_def = Section(
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description='Host component of the solid solution composed of crystalline '
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'substance.',
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a_eln=ELNAnnotation(
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properties=SectionProperties(
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order=[
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'name',
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'system',
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'molecular_formula',
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]
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)
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),
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)
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system = Quantity(
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type=CrystallinePureSubstance,
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a_eln=dict(component='ReferenceEditQuantity'),
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)
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molecular_formula = Quantity(
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type=str,
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description='The molecular formula of the host component, e.g., LiYF4.',
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a_eln=dict(component='StringEditQuantity'),
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)
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def normalize(self, archive, logger: 'BoundLogger') -> None:
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super().normalize(archive, logger)
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try:
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self.molecular_formula = self.system.pure_substance.molecular_formula
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except AttributeError:
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pass
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class DopantComponent(SystemComponent):
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m_def = Section(
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description='Dopant component of the solid solution composed of a crystalline '
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'substance.',
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a_eln=ELNAnnotation(
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properties=SectionProperties(
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order=[
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'name',
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'system',
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'molecular_formula',
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]
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)
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),
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)
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system = Quantity(
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type=CrystallinePureSubstance,
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a_eln=dict(component='ReferenceEditQuantity'),
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)
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molecular_formula = Quantity(
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type=str,
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description='The molecular formula of the dopant component, e.g., Pr.',
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a_eln=dict(component='StringEditQuantity'),
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)
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def normalize(self, archive, logger: 'BoundLogger') -> None:
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super().normalize(archive, logger)
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try:
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self.molecular_formula = self.system.pure_substance.molecular_formula
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except AttributeError:
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pass
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class ElementalDopantComponent(DopantComponent):
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m_def = Section(
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description=(
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'An elemental dopant added in small quantities which substitutes another '
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'element in the solvent.'
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),
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a_eln=ELNAnnotation(
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properties=SectionProperties(
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order=[
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'name',
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'system',
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'molecular_formula',
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'substitution_element',
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'nominal_concentration',
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'measured_concentration',
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],
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)
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),
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)
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molecular_formula = Quantity(
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type=MEnum(chemical_symbols[1:]),
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description='The symbol of the dopant element, e.g., Pr.',
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a_eln=dict(component='AutocompleteEditQuantity'),
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)
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substitution_element = Quantity(
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type=MEnum(chemical_symbols[1:]),
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description=('The element in the host crystal that is being replaced.'),
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a_eln=dict(component='AutocompleteEditQuantity'),
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)
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nominal_concentration = Quantity(
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type=np.float64,
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description=(
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'Atomic percentage of solute element with respect to the '
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'substitution element determined during preparation. '
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'For example, 1 at.% Pr-doped LiYF4 is equivalent to Li(Pr0.01Y0.99)F4'
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),
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a_eln={
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'component': 'NumberEditQuantity',
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'minValue': 0,
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'maxValue': 100,
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},
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unit='dimensionless',
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)
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measured_concentration = Quantity(
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type=np.float64,
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description=(
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'Atomic percentage of solute element with respect to the '
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'substitution element measured in the prepared sample using techniques like '
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'Transmission Spectrophotometry.'
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),
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a_eln={
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'component': 'NumberEditQuantity',
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'minValue': 0,
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'maxValue': 100,
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},
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unit='dimensionless',
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)
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class SolidSolution(CompositeSystem):
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m_def = Section(
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links=['https://doi.org/10.1351/goldbook.M03940'],
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description=(
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'A crystal containing other constituents (solutes) which fit into and '
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'are distributed in the lattice of the host crystal (solvent).'
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),
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a_eln=ELNAnnotation(
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properties=SectionProperties(
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order=[
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'name',
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'molecular_formula',
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'host',
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'dopants',
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'elemental_composition',
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'crystal_properties',
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],
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visible=Filter(
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exclude=[
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'datetime',
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'lab_id',
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'description',
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'components',
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],
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),
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),
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),
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)
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molecular_formula = Quantity(
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type=str,
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description='Molecular formula of the solid solution. Dopant concentrations is '
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'expressed relatively as fraction of substitution element. For example, '
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'1 at.% Pr-doped LiYF4 is expressed as Li(Pr0.01Y0.99)F4',
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a_eln={'component': 'StringEditQuantity'},
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)
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host = SubSection(
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section_def=HostComponent,
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)
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dopants = SubSection(
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section_def=ElementalDopantComponent,
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repeats=True,
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)
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crystal_properties = SubSection(
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section_def=CrystalProperties,
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description='Properties of the crystalline structure.',
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)
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def adjust_composition_for_dopant_substitution(self, archive, logger):
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"""
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Adjust the atomic fraction of each element based on each dopant substitution.
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Dopants are solutes which are added in small quantities to the solvent.
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Dopant concentration is given as a percentage of the substitution element. It can
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be the measured concentration (first preference) or the nominal concentration.
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"""
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if not self.host:
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return
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if not self.dopants:
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return
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for dopant in self.dopants:
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if dopant.measured_concentration is not None:
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dopant_concentration = dopant.measured_concentration
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elif dopant.nominal_concentration is not None:
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dopant_concentration = dopant.nominal_concentration
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else:
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continue
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# find the substitution element and the dopant in the elemental composition
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# and adjust their atomic fractions
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for element_substituted in self.elemental_composition:
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if element_substituted.element == dopant.substitution_element:
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for element_substituting in self.elemental_composition:
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if element_substituting.element == dopant.molecular_formula:
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element_substituting.atomic_fraction = (
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dopant_concentration
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/ 100
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* element_substituted.atomic_fraction
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)
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element_substituted.atomic_fraction -= (
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element_substituting.atomic_fraction
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)
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break
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break
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@staticmethod
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def derive_molecular_formula(host, dopants):
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"""
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Derive the molecular formula of the solid solution based on dopant substitutions.
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"""
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if host.molecular_formula:
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molecular_formula = host.molecular_formula
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else:
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return ''
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for dopant in dopants:
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if dopant.molecular_formula is None or dopant.substitution_element is None:
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continue
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if dopant.measured_concentration is not None:
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dopant_concentration = dopant.measured_concentration
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elif dopant.nominal_concentration is not None:
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dopant_concentration = dopant.nominal_concentration
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else:
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continue
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fractional_symbol = (
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'('
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+ dopant.molecular_formula
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+ str('{:.2f}'.format(dopant_concentration.magnitude / 100))
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+ ' '
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+ dopant.substitution_element
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+ str('{:.2f}'.format(1 - dopant_concentration.magnitude / 100))
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+ ')'
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)
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molecular_formula = molecular_formula.replace(
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dopant.substitution_element, fractional_symbol
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)
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return molecular_formula
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def normalize(self, archive, logger: 'BoundLogger') -> None:
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self.components = []
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self.elemental_composition = []
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if self.host:
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self.components.append(self.host)
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if self.dopants:
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for dopant in self.dopants:
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self.components.append(dopant)
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super().normalize(archive, logger)
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if self.host and self.dopants:
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self.adjust_composition_for_dopant_substitution(archive, logger)
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# reset the mass fractions and recalculate them
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for element in self.elemental_composition:
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element.mass_fraction = None
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super().normalize(archive, logger)
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self.molecular_formula = self.derive_molecular_formula(
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host=self.host, dopants=self.dopants
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)

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