nomad-material-processing 1.0.4__tar.gz → 1.0.5__tar.gz

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nomad-material-processing
-Version: 1.0.4
+Version: 1.0.5
 Summary: A plugin for NOMAD containing base sections for material processing.
 Author: Andrea Albino, Sebastian Brückner, Michael Götte, Ahmed Ilyas, Sarthak Kapoor, José A. Márquez, Hampus Näsström, Markus Scheidgen
 Author-email: fairmat@physik.hu-berlin.de

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/docs/explanation/schemas.md

@@ -123,21 +123,21 @@ The `nomad_material_processing.vapor_deposition.pvd.mbe` module uses the thermal
 source and also adds a plasma source.
 
 
-### nomad_material_processing.solution.general
+### Solutions
 
-The main entry sections in this module are
+`nomad_material_processing.solution.general` provides
 [`Solution`](#nomad_material_processing.solution.general.Solution) and
-[`SolutionPreparation`](#nomad_material_processing.solution.general.SolutionPreparation) which can
-be used to create NOMAD
+[`SolutionPreparation`](#nomad_material_processing.solution.general.SolutionPreparation)
+entry sections which can be used to create NOMAD
 [entries](https://nomad-lab.eu/prod/v1/docs/reference/glossary.html#entry).
-There's a long list of other auxiliary sections supporting these entry section which
+It also contains other auxiliary sections supporting these entry section which
 can be accessed in the
 [metainfo browser](https://nomad-lab.eu/prod/v1/oasis/gui/analyze/metainfo/nomad_material_processing)
 by searching for: `"nomad_material_processing.solution.general"`
 
-#### `nomad_material_processing.solution.general.Solution`
+#### Solution
 
-Describes liquid solutions by extending the
+`nomad_material_processing.solution.general.Solution` describes liquid solutions by extending the
 [`CompositeSystem`](https://nomad-lab.eu/prod/v1/docs/howto/customization/base_sections.html#system) with quantities: _pH_, _mass_,
 _calculated_volume_, _measured_volume_, _density_, and sub-sections:
 _solvents_, _solutes_, and _solution_storage_.
@@ -172,14 +172,24 @@ _calculated_volume_ of the solution. The component can either nest a
 sub-section describing its composition, or can be another `Solution` entry connected
 via reference.
 These options are are handled by
-`SolutionComponent` and `SolutionComponentReference` sections respectively. Let's take a closer look at each of them.
+`SolutionComponent` and `SolutionComponentReference` sections respectively. 
 
-`SolutionComponent` extends `PureSubstanceComponent` with quantities:
-_component_role_, _mass_, _volume_, _density_, and sub-section: _molar_concentration_.
+Let's take a closer look at each of them.
+
+__`SolutionComponent`__ extends `PureSubstanceComponent` with quantities:
+_component_role_, _mass_, _volume_, _density_, _amount_of_substance_ (in moles),
+and sub-section: _molar_concentration_.
 The _pure_substance_ sub-section inherited from `PureSubstanceComponent` specifies the
-chemical compound. This information along with the mass of the component and
+chemical compound. This information along with the amount of the component and
 total volume of the solution is used to automatically determine the molar concentration of
 the component, populating the corresponding sub-section.
+
+If not provided, _amount_of_substance_ can be determined from _mass_ and 
+_pure_substance.molecular_mass_.
+On other hand, if _amount_of_substance_ is available, but _mass_ is missing, it can be 
+determined using _amount_of_substance_ and _pure_substance.molecular_mass_.
+_mass_ can also be determined if _volume_ and _density_ are available.
+
 Based on the _component_role_, the components are copied over to either
 `Solution.solvents` or `Solution.solutes`.
 
@@ -189,10 +199,11 @@ class SolutionComponent(PureSubstanceComponent):
     mass: float
     volume: float
     density: float
+    amount_of_substance: float
     molar_concentration: MolarConcentration
 ```
 
-`SolutionComponentReference` makes a reference to another `Solution` entry and specifies
+__`SolutionComponentReference`__ makes a reference to another `Solution` entry and specifies
 the amount used. Based on this, _solutes_ and _solvents_ of the referenced solution are
 copied over to the first solution. Their mass and volume are adjusted based on the
 amount of the referenced solution used.
@@ -212,9 +223,10 @@ combined into one.
 The _solution_storage_ uses `SolutionStorage` section to describe storage conditions
 , i.e., temperature and atmosphere, along with preparation and expiry dates.
 
-#### `nomad_material_processing.solution.general.SolutionPreparation`
+#### SolutionPreparation
 
-Describes the steps of solution preparation by extending
+`nomad_material_processing.solution.general.SolutionPreparation`
+describes the steps of solution preparation by extending
 [`Process`](https://nomad-lab.eu/prod/v1/docs/howto/customization/base_sections.html#process).
 Based on the steps added, it also creates a `Solution` entry and references it under the
 _solution_ sub-section.

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/src/nomad_material_processing/general.py

@@ -757,6 +757,7 @@ class ElectronicProperties(ArchiveSection):
             'P-type',
             'N-type',
             'Semi-insulating',
+            'Insulating',
         ),
         description="""The type of semiconductor, N-type being electrons
         the majority carriers and P-type being holes the majority carriers.""",

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/src/nomad_material_processing/solution/general.py

@@ -3,6 +3,7 @@ from typing import TYPE_CHECKING, Union
 from nomad.datamodel.data import (
     ArchiveSection,
     EntryData,
+    EntryDataCategory,
 )
 from nomad.datamodel.metainfo.annotations import (
     ELNAnnotation,
@@ -21,6 +22,7 @@ from nomad.datamodel.metainfo.basesections import (
     SystemComponent,
 )
 from nomad.metainfo import (
+    Category,
     Datetime,
     MEnum,
     Quantity,
@@ -52,6 +54,17 @@ configuration = config.get_plugin_entry_point(
 )
 
 
+class SolutionCategory(EntryDataCategory):
+    """
+    Category for entry schemas related to solutions.
+    """
+
+    m_def = Category(
+        label='Solutions',
+        categories=[EntryDataCategory],
+    )
+
+
 class MolarConcentration(ArchiveSection):
     """
     The molar concentration of a component in a solution.
@@ -62,10 +75,9 @@ class MolarConcentration(ArchiveSection):
     )
     calculated_concentration = Quantity(
         type=float,
-        description=(
-            'The expected concentration calculated from the component moles and '
-            'total volume.'
-        ),
+        description="""
+        The expected concentration calculated from the component moles and total volume.
+        """,
         a_eln=ELNAnnotation(
             defaultDisplayUnit='mol / liter',
         ),
@@ -73,10 +85,9 @@ class MolarConcentration(ArchiveSection):
     )
     measured_concentration = Quantity(
         type=float,
-        description=(
-            """The concentration observed or measured
-            with some characterization technique."""
-        ),
+        description="""
+        The concentration observed or measured with some characterization technique.
+        """,
         a_eln=ELNAnnotation(
             component='NumberEditQuantity',
             defaultDisplayUnit='mol / liter',
@@ -157,7 +168,6 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
     Section for a component added to the solution.
     """
 
-    # TODO get the density of the component automatically if not provided
     m_def = Section(
         description='A component added to the solution.',
         a_eln=ELNAnnotation(
@@ -198,7 +208,11 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
     )
     mass = Quantity(
         type=float,
-        description='The mass of the component without the container.',
+        description="""
+        The mass of the component without the container. Can be calculated automatically
+        if `volume` and `density` are available or if `amount_of_substance`
+        and `pure_substance.molecular_mass` are available.
+        """,
         a_eln=ELNAnnotation(
             component='NumberEditQuantity',
             defaultDisplayUnit='gram',
@@ -206,15 +220,29 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
         ),
         unit='kilogram',
     )
+    amount_of_substance = Quantity(
+        link='https://doi.org/10.1351/goldbook.A00297',
+        type=float,
+        description="""
+        The number of elementary entities of the given substance. Can be calculated
+        automatically if `mass` and `pure_substance.molecular_mass` are available.
+        """,
+        a_eln=ELNAnnotation(
+            component='NumberEditQuantity',
+            defaultDisplayUnit='mole',
+            minValue=0,
+        ),
+        unit='mole',
+    )
     density = Quantity(
         type=float,
         description='The density of the liquid component.',
         a_eln=ELNAnnotation(
             component='NumberEditQuantity',
-            defaultDisplayUnit='gram / liter',
+            defaultDisplayUnit='gram / milliliter',
             minValue=0,
         ),
-        unit='kilogram / liter',
+        unit='gram / milliliter',
     )
     molar_concentration = SubSection(section_def=MolarConcentration)
     pure_substance = SubSection(section_def=PubChemPureSubstanceSection)
@@ -254,8 +282,8 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
         self, volume: Quantity, logger: 'BoundLogger' = None
     ) -> None:
         """
-        Calculate the molar concentration of the component
-        in a given volume of solution.
+        Calculate the molar concentration of the component in a given volume of
+        solution.
 
         Args:
             volume (Quantity): The volume of the solution.
@@ -270,9 +298,10 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
             return
         if not self.molar_concentration:
             self.molar_concentration = MolarConcentration()
-        moles = self._calculate_moles(logger)
-        if moles:
-            self.molar_concentration.calculated_concentration = moles / volume
+        if self.amount_of_substance:
+            self.molar_concentration.calculated_concentration = (
+                self.amount_of_substance / volume
+            )
 
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         """
@@ -288,6 +317,12 @@ class SolutionComponent(PureSubstanceComponent, BaseSolutionComponent):
             self.pure_substance.normalize(archive, logger)
         if self.volume and self.density:
             self.mass = self.volume * self.density
+        if self.mass and self.pure_substance and not self.amount_of_substance:
+            self.amount_of_substance = self._calculate_moles(logger)
+        if self.amount_of_substance and self.pure_substance and not self.mass:
+            self.mass = self.amount_of_substance * (
+                self.pure_substance.molecular_mass * ureg.N_A
+            )
         super().normalize(archive, logger)
 
 
@@ -298,6 +333,7 @@ class Solution(CompositeSystem, EntryData):
 
     # TODO make the solvents, solutes, and elemental_composition subsection noneditable.
     m_def = Section(
+        categories=[SolutionCategory],
         description='A homogeneous liquid mixture composed of two or more substances.',
         a_eln=ELNAnnotation(
             properties=SectionProperties(
@@ -334,7 +370,7 @@ class Solution(CompositeSystem, EntryData):
         a_eln=ELNAnnotation(
             defaultDisplayUnit='gram / milliliter',
         ),
-        unit='kilogram / liter',
+        unit='gram / milliliter',
     )
     mass = Quantity(
         description='The mass of the solution.',
@@ -412,7 +448,7 @@ class Solution(CompositeSystem, EntryData):
                 continue
             comparison_key = component.pure_substance.pub_chem_cid
             if comparison_key in combined_components:
-                for prop in ['mass', 'volume']:
+                for prop in ['mass', 'volume', 'amount_of_substance']:
                     val1 = getattr(combined_components[comparison_key], prop, None)
                     val2 = getattr(component, prop, None)
                     if val1 and val2:
@@ -503,6 +539,8 @@ class Solution(CompositeSystem, EntryData):
                                 self.solvents[-1].volume *= scaler
                             if self.solvents[-1].mass:
                                 self.solvents[-1].mass *= scaler
+                            if self.solvents[-1].amount_of_substance:
+                                self.solvents[-1].amount_of_substance *= scaler
                     if component.system.solutes:
                         for solute in component.system.solutes:
                             self.solutes.append(solute.m_copy(deep=True))
@@ -510,6 +548,8 @@ class Solution(CompositeSystem, EntryData):
                                 self.solutes[-1].volume *= scaler
                             if self.solutes[-1].mass:
                                 self.solutes[-1].mass *= scaler
+                            if self.solutes[-1].amount_of_substance:
+                                self.solutes[-1].amount_of_substance *= scaler
 
         self.solvents = self.combine_components(self.solvents, logger)
         self.solutes = self.combine_components(self.solutes, logger)
@@ -827,6 +867,7 @@ class SolutionPreparation(Process, EntryData):
 
     # TODO populate the instruments section based on the steps.methodology.instrument
     m_def = Section(
+        categories=[SolutionCategory],
         description='Section for describing steps of solution preparation.',
         a_eln=ELNAnnotation(
             properties=SectionProperties(

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/src/nomad_material_processing/vapor_deposition/general.py

@@ -31,6 +31,7 @@ from nomad.datamodel.metainfo.basesections import (
     Component,
     CompositeSystemReference,
     Entity,
+    EntityReference,
     PubChemPureSubstanceSection,
     PureSubstanceSection,
 )
@@ -118,6 +119,21 @@ class InsertReduction(Entity):
     )
 
 
+class InsertReductionReference(EntityReference):
+    """
+    A section used for referencing a FilledSubstrateHolderPDI.
+    """
+
+    reference = Quantity(
+        type=InsertReduction,
+        description='Optional description of insert if used.',
+        a_eln=ELNAnnotation(
+            component='ReferenceEditQuantity',
+            label='Insert Reduction Reference',
+        ),
+    )
+
+
 class SubstrateHolderPosition(ArchiveSection):
     """
     One casing position of the substrate holder.
@@ -159,14 +175,6 @@ class SubstrateHolderPosition(ArchiveSection):
     slot_geometry = SubSection(
         section_def=Geometry,
     )
-    insert_reduction = Quantity(
-        type=InsertReduction,
-        description='Optional description of insert if used.',
-        a_eln=ELNAnnotation(
-            component='ReferenceEditQuantity',
-            label='ThinFilmStackMbe Reference',
-        ),
-    )
 
 
 class SubstrateHolder(Entity):
@@ -189,10 +197,10 @@ class SubstrateHolder(Entity):
         The lab ID of the substrate holder.
         """,
         a_eln=ELNAnnotation(
-            component=ELNComponentEnum.StringEditQuantity,
+            component=ELNComponentEnum.StringEditQuantity, label='holder_id'
         ),
     )
-    material = SubSection(section_def=PubChemPureSubstanceSection, repeats=True)
+    holder_material = SubSection(section_def=PubChemPureSubstanceSection, repeats=True)
     thickness = Quantity(
         type=float,
         unit='meter',
@@ -243,6 +251,12 @@ class FilledSubstrateHolderPosition(SubstrateHolderPosition):
     One casing position of the filled substrate holder.
     """
 
+    insert_reduction = SubSection(
+        section_def=InsertReductionReference,
+        description="""
+        The Insert reduction placed in this position.
+        """,
+    )
     substrate = SubSection(
         section_def=CompositeSystemReference,
         description="""
@@ -261,7 +275,7 @@ class FilledSubstrateHolder(SubstrateHolder):
         description='A reference to an empty substrate holder.',
         a_eln=ELNAnnotation(
             component='ReferenceEditQuantity',
-            label='ThinFilmStackMbe Reference',
+            label='Empty Substrate Holder Reference',
         ),
     )
     positions = SubSection(

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/src/nomad_material_processing.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: nomad-material-processing
-Version: 1.0.4
+Version: 1.0.5
 Summary: A plugin for NOMAD containing base sections for material processing.
 Author: Andrea Albino, Sebastian Brückner, Michael Götte, Ahmed Ilyas, Sarthak Kapoor, José A. Márquez, Hampus Näsström, Markus Scheidgen
 Author-email: fairmat@physik.hu-berlin.de

{nomad_material_processing-1.0.4 → nomad_material_processing-1.0.5}/tests/solution/test_solution_schema.py

@@ -58,12 +58,16 @@ def test_solution():
     starter_water_concentration = starter_solution_archive.data.solvents[
         0
     ].molar_concentration.calculated_concentration
+    starter_water_amount = starter_solution_archive.data.solvents[0].amount_of_substance
     starter_salt_concentration = starter_solution_archive.data.solutes[
         0
     ].molar_concentration.calculated_concentration
     starter_salt_mass = starter_solution_archive.data.solutes[0].mass
 
     assert pytest.approx(starter_water_concentration, 1e-3) == 55.523 * ureg('mol/l')
+    assert pytest.approx(starter_water_amount, 1e-3) == 0.5 * ureg('l') * 55.523 * ureg(
+        'mol/l'
+    )
     assert pytest.approx(starter_salt_concentration, 1e-3) == 0.345 * ureg('mol/l')
     assert pytest.approx(starter_salt_mass, 1e-3) == 0.01 * ureg('kg')
 
@@ -90,6 +94,13 @@ def test_solution():
         )
         == starter_water_concentration
     )
+    assert (
+        pytest.approx(
+            main_solution_archive.data.solvents[0].amount_of_substance,
+            1e-3,
+        )
+        == starter_water_amount / 5
+    )
     assert (
         pytest.approx(
             main_solution_archive.data.solutes[
@@ -129,6 +140,13 @@ def test_solution():
         )
         == starter_water_concentration
     )
+    assert (
+        pytest.approx(
+            main_solution_archive.data.solvents[0].amount_of_substance,
+            1e-3,
+        )
+        == (starter_water_amount / 5) * 2
+    )
     assert (
         pytest.approx(
             main_solution_archive.data.solutes[
@@ -154,6 +172,13 @@ def test_solution():
         )
         == starter_water_concentration
     )
+    assert (
+        pytest.approx(
+            starter_solution_archive.data.solvents[0].amount_of_substance,
+            1e-3,
+        )
+        == starter_water_amount
+    )
     assert (
         pytest.approx(
             starter_solution_archive.data.solutes[