create substrate and characterization modules in IKZ_plugin

IKZ_plugin/src/basesections/__init__.py

@@ -1,12 +1,85 @@
 import json
 
-from nomad.metainfo import (
-    Package, Quantity, SubSection, Section, Category)
+
 from nomad.datamodel.data import EntryData, EntryDataCategory
-#from nomad.datamodel.metainfo.workflow import Link
-from nomad.datamodel.metainfo.eln import Entity, Activity, SampleID
-from nomad.datamodel.util import parse_path
+import numpy as np
+import plotly.express as px
+from plotly.subplots import make_subplots
+from ase.data import chemical_symbols
+from nomad.datamodel.metainfo.basesections import (
+    ElementalComposition,
+    Activity,
+    PureSubstance,
+    ProcessStep,
+    CompositeSystem,
+    Measurement,
+    MeasurementResult,
+    Process,
+    PureSubstanceComponent,
+    PureSubstanceSection,
+    EntityReference,
+    CompositeSystemReference,
+    PubChemPureSubstanceSection,
+    SectionReference,
+    Experiment,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    SectionProperties,
+)
+from nomad.parsing.tabular import TableData
+from structlog.stdlib import (
+    BoundLogger,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    ELNComponentEnum,
+)
+from nomad.metainfo import Package, Quantity, SubSection, MEnum, Datetime, Section, Category
+from nomad.datamodel.data import EntryData, ArchiveSection, Author
+from nomad.search import search, MetadataPagination
+
+from nomad.datamodel.metainfo.plot import PlotSection, PlotlyFigure
+
+from laytec_epitt import LayTecEpiTTMeasurement
+from hall import HallMeasurement
+from basesections import IKZMOVPECategory, IKZMOVPE1Category, IKZMOVPE2Category
+from nomad_material_processing import (
+    SubstrateReference,
+    CrystallineSubstrate,
+    Miscut,
+    SubstrateCrystalProperties,
+    Dopant,
+    Geometry,
+    ThinFilm,
+    ThinFilmStack,
+    ThinFilmStackReference,
+)
+from nomad_material_processing.vapor_deposition import (
+    VaporDeposition,
+    VaporDepositionSource,
+    VaporDepositionStep,
+    SampleParameters,
+    SubstrateTemperature,
+    ChamberEnvironment,
+    GasFlow,
+    Pressure,
+    SubstrateHeater,
+)
 
+from nomad.datamodel.metainfo.workflow import (
+    Link,
+    Task,
+)
+from nomad_material_processing.chemical_vapor_deposition import (
+    CVDBubbler,
+    CVDVaporRate,
+    CVDSource,
+)
+
+from nomad_measurements import (
+    ActivityReference,
+)
 
 m_package = Package(name='basesections_IKZ')
 
@@ -34,6 +107,74 @@ class IKZHallCategory(EntryDataCategory):
     m_def = Category(label='Hall', categories=[EntryDataCategory, IKZCategory])
 
 
+class Etching(Process, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln=None,
+        categories=[IKZCategory],
+    )
+    method = Quantity(
+        type=str,
+        default="Etching (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        description="FILL",
+        a_eln={"component": "DateTimeEditQuantity", "label": "deposition_date"},
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description="FILL THE DESCRIPTION",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "celsius"},
+        unit="celsius",
+    )
+    elapsed_time = Quantity(
+        type=np.float64,
+        description="Past time since process started (minutes)",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "minute"},
+        unit="minute",
+    )
+    etching_reagents = SubSection(section_def=CompositeSystem, repeats=True)
+
+
+class Annealing(Process, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln=None,
+        categories=[IKZCategory],
+    )
+    method = Quantity(
+        type=str,
+        default="Annealing (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        description="FILL",
+        a_eln={"component": "DateTimeEditQuantity", "label": "deposition_date"},
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description="FILL THE DESCRIPTION",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "celsius"},
+        unit="celsius",
+    )
+    elapsed_time = Quantity(
+        type=np.float64,
+        description="Past time since process started (minutes)",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "minute"},
+        unit="minute",
+    )
+    anealing_reagents = SubSection(
+        section_def=CompositeSystemReference,
+    )
+
+
 # class CollectionOfSystems(Entity, EntryData):
 #     '''
 #     A base class for a batch of materials. Each component of the batch is

IKZ_plugin/src/characterization/__init__.py

@@ -0,0 +1,18 @@
+# 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.
+#
+
+from .schema import *

IKZ_plugin/src/characterization/nomad_plugin.yaml

@@ -0,0 +1,5 @@
+plugin_type: schema
+name: NOMAD's example schema plugin
+description: |
+  This is a simple hello world schema. This is meant as a template.
+  Fork the github project to create your own schemas.

IKZ_plugin/src/characterization/schema.py

@@ -0,0 +1,183 @@
+import numpy as np
+import plotly.express as px
+from plotly.subplots import make_subplots
+from ase.data import chemical_symbols
+from nomad.datamodel.metainfo.basesections import (
+    ElementalComposition,
+    Activity,
+    PureSubstance,
+    ProcessStep,
+    CompositeSystem,
+    Measurement,
+    MeasurementResult,
+    Process,
+    PureSubstanceComponent,
+    PureSubstanceSection,
+    EntityReference,
+    CompositeSystemReference,
+    PubChemPureSubstanceSection,
+    SectionReference,
+    Experiment,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    SectionProperties,
+)
+from nomad.parsing.tabular import TableData
+from structlog.stdlib import (
+    BoundLogger,
+)
+from nomad.datamodel.metainfo.annotations import (
+    ELNAnnotation,
+    ELNComponentEnum,
+)
+from nomad.metainfo import Package, Quantity, SubSection, MEnum, Datetime, Section
+from nomad.datamodel.data import EntryData, ArchiveSection, Author
+from nomad.search import search, MetadataPagination
+
+from nomad.datamodel.metainfo.plot import PlotSection, PlotlyFigure
+
+from laytec_epitt import LayTecEpiTTMeasurement
+from hall import HallMeasurement
+from basesections import IKZCategory
+from nomad_material_processing import (
+    SubstrateReference,
+    CrystallineSubstrate,
+    Miscut,
+    SubstrateCrystalProperties,
+    Dopant,
+    Geometry,
+    Parallelepiped,
+    ThinFilm,
+    ThinFilmStack,
+    ThinFilmStackReference,
+)
+
+from nomad.datamodel.metainfo.workflow import (
+    Link,
+    Task,
+)
+from nomad_material_processing.chemical_vapor_deposition import (
+    CVDBubbler,
+    CVDVaporRate,
+    CVDSource,
+)
+
+from nomad_measurements import (
+    ActivityReference,
+)
+
+m_package = Package(name="characterization_IKZ")
+
+
+class AFMresults(MeasurementResult):
+    """
+    The results of an AFM measurement
+    """
+
+    roughness = Quantity(
+        type=np.float64,
+        description="RMS roughness value obtained by AFM",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "picometer"},
+        unit="picometer",
+    )
+    surface_features = Quantity(
+        type=MEnum(["Step Flow", "Step Bunching", "2D Island"]),
+        a_eln={"component": "EnumEditQuantity"},
+    )
+    scale = Quantity(
+        type=np.float64,
+        description="scale of the image, to be multiplied by 5 to know the image size",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "nanometer"},
+        unit="nanometer",
+    )
+    image = Quantity(
+        type=str,
+        description="image showing the thickness measurement points",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    crop_image = Quantity(
+        type=str,
+        description="crop image ready to be used for AI-based analysis",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+
+
+class AFMmeasurement(Measurement, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln={"hide": ["steps"]},
+        categories=[IKZCategory],
+        label="AFM",
+    )
+
+    method = Quantity(
+        type=str,
+        default="AFM (IKZ MOVPE)",
+    )
+    description = Quantity(
+        type=str,
+        a_eln={"component": "StringEditQuantity"},
+    )
+    datetime = Quantity(
+        type=Datetime,
+        a_eln={"component": "DateTimeEditQuantity"},
+    )
+    results = SubSection(
+        section_def=AFMresults,
+        repeats=True,
+    )
+
+
+class LiMiresults(MeasurementResult):
+    """
+    The results of a Light Microscope measurement
+    """
+
+    image = Quantity(
+        type=str,
+        description="image showing the thickness measurement points",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    crop_image = Quantity(
+        type=str,
+        description="crop image ready to be used for AI-based analysis",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    scale = Quantity(
+        type=np.float64,
+        description="scale of the image",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "micrometer"},
+        unit="micrometer",
+    )
+
+
+class LightMicroscope(Measurement, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln={"hide": ["steps"]},
+        categories=[IKZCategory],
+        label="Light Microscope",
+    )
+    method = Quantity(
+        type=str,
+        default="Light Microscope (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        a_eln={"component": "DateTimeEditQuantity"},
+    )
+    results = SubSection(
+        section_def=LiMiresults,
+        repeats=True,
+    )