nomad-material-processing 1.0.6__tar.gz → 1.0.7__tar.gz

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-material-processing
-Version: 1.0.6
+Version: 1.0.7
 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
@@ -216,6 +216,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nomad-lab>=1.3.14
@@ -223,7 +224,7 @@ Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: structlog; extra == "dev"
-Requires-Dist: nomad-docs>=0.1.3; extra == "dev"
+Requires-Dist: nomad-docs>=2.0.1; extra == "dev"
 Requires-Dist: mkdocs; extra == "dev"
 Requires-Dist: mkdocs-material>=9.0; extra == "dev"
 Requires-Dist: pymdown-extensions; extra == "dev"

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/mkdocs.yml

@@ -17,23 +17,23 @@ nav:
   - Reference: 
     - Glossary: reference/references.md
     - Schemas: 
-      - reference/schemas/general.md
-      - reference/schemas/combinatorial.md
-      - reference/schemas/epitaxy.md
-      - reference/schemas/crystal_growth.md
+      - General: reference/schemas/general.md
+      - Combinatorial: reference/schemas/combinatorial.md
+      - Epitaxy: reference/schemas/epitaxy.md
+      - Crystal Growth: reference/schemas/crystal_growth.md
       - Solution:
-        - reference/schemas/solution/general.md
+        - General: reference/schemas/solution/general.md
       - Vapor Deposition:
-        - reference/schemas/vapor_deposition/general.md
+        - General: reference/schemas/vapor_deposition/general.md
         - CVD:
-          - reference/schemas/vapor_deposition/cvd/general.md
-          - reference/schemas/vapor_deposition/cvd/movpe.md
+          - General: reference/schemas/vapor_deposition/cvd/general.md
+          - MOVPE: reference/schemas/vapor_deposition/cvd/movpe.md
         - PVD:
-          - reference/schemas/vapor_deposition/pvd/general.md
-          - reference/schemas/vapor_deposition/pvd/sputtering.md
-          - reference/schemas/vapor_deposition/pvd/thermal.md
-          - reference/schemas/vapor_deposition/pvd/pld.md
-          - reference/schemas/vapor_deposition/pvd/mbe.md
+          - General: reference/schemas/vapor_deposition/pvd/general.md
+          - Sputtering: reference/schemas/vapor_deposition/pvd/sputtering.md
+          - Thermal Evaporation: reference/schemas/vapor_deposition/pvd/thermal.md
+          - Pulsed Laser Deposition: reference/schemas/vapor_deposition/pvd/pld.md
+          - Molecular Beam Epitaxy: reference/schemas/vapor_deposition/pvd/mbe.md
   - Tutorials: tutorial/tutorial.md
   - Contact: contact.md
 plugins:
@@ -77,5 +77,4 @@ extra_css:
   - stylesheets/extra.css
 extra_javascript:
   - javascript.js
-  # - https://polyfill.io/v3/polyfill.min.js?features=es6
-  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/pyproject.toml

@@ -19,6 +19,7 @@ name = "nomad-material-processing"
 dynamic = ["version"]
 description = "A plugin for NOMAD containing base sections for material processing."
 readme = "README.md"
+requires-python = ">=3.10"
 authors = [
     { name = "Andrea Albino" },
     { name = "Sebastian Brückner" },
@@ -51,7 +52,7 @@ dev = [
     "pytest",
     "ruff",
     "structlog",
-    "nomad-docs>=0.1.3",
+    "nomad-docs>=2.0.1",
     "mkdocs",
     "mkdocs-material>=9.0",
     "pymdown-extensions",

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/src/nomad_material_processing/general.py

@@ -706,6 +706,29 @@ class CrystalProperties(ArchiveSection):
     parameters, and the specific arrangement of atoms within the crystal lattice.
     """
 
+    bravais_lattices = Quantity(
+        type=MEnum(
+            'Triclinic',
+            'Monoclinic Primitive',
+            'Monoclinic Base Centered',
+            'Orthorhombic Primitive',
+            'Orthorhombic Base Centered',
+            'Orthorhombic Body Centered',
+            'Orthorhombic Face Centered',
+            'Tetragonal Primitive',
+            'Tetragonal Body Centered',
+            'Cubic Primitive',
+            'Cubic Body Centered',
+            'Cubic Face Centered',
+            'Rhombohedral',
+            'Hexagonal',
+        ),
+        description='The Bravais lattice of the crystal structure.',
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.EnumEditQuantity,
+        ),
+    )
+
 
 class SubstrateCrystalProperties(CrystalProperties):
     """
@@ -715,21 +738,26 @@ class SubstrateCrystalProperties(CrystalProperties):
     bravais_lattices = Quantity(
         type=MEnum(
             'Triclinic',
-            'Monoclinic Simple',
+            'Monoclinic Primitive',
             'Monoclinic Base Centered',
-            'Orthorhombic Simple',
+            'Orthorhombic Primitive',
             'Orthorhombic Base Centered',
             'Orthorhombic Body Centered',
             'Orthorhombic Face Centered',
-            'Tetragonal Simple',
+            'Tetragonal Primitive',
             'Tetragonal Body Centered',
-            'Cubic Simple',
+            'Cubic Primitive',
             'Cubic Body Centered',
             'Cubic Face Centered',
-            'Trigonal',
+            'Rhombohedral',
             'Hexagonal',
+            'Monoclinic Simple',  # Incorrect term, normalizes to Monoclinic Primitive
+            'Orthorhombic Simple',  # Incorrect term, norm. to Orthorhombic Primitive
+            'Tetragonal Simple',  # Incorrect term, normalizes to Tetragonal Primitive
+            'Cubic Simple',  # Incorrect term, normalizes to Cubic Primitive
+            'Trigonal',  # Incorrect term, normalizes to Rhombohedral
         ),
-        description='The crystal system of the substrate.',
+        description='The Bravais lattice of the crystal structure.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.EnumEditQuantity,
         ),
@@ -745,6 +773,30 @@ class SubstrateCrystalProperties(CrystalProperties):
         """,
     )
 
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
+        """
+        The normalizer for the `SubstrateCrystalProperties` class.
+
+        Args:
+            archive (EntryArchive): The archive containing the section that is being
+            normalized.
+            logger (BoundLogger): A structlog logger.
+        """
+        old_terminologies = {
+            'Monoclinic Simple': 'Monoclinic Primitive',
+            'Orthorhombic Simple': 'Orthorhombic Primitive',
+            'Tetragonal Simple': 'Tetragonal Primitive',
+            'Cubic Simple': 'Cubic Primitive',
+            'Trigonal': 'Rhombohedral',
+        }
+        if self.bravais_lattices in old_terminologies:
+            logger.warning(
+                f"Bravais lattice '{self.bravais_lattices}' is incorrect terminology. "
+                f"Normalizing to '{old_terminologies[self.bravais_lattices]}'."
+            )
+            self.bravais_lattices = old_terminologies[self.bravais_lattices]
+        super().normalize(archive, logger)
+
 
 class ElectronicProperties(ArchiveSection):
     """

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/src/nomad_material_processing.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-material-processing
-Version: 1.0.6
+Version: 1.0.7
 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
@@ -216,6 +216,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: nomad-lab>=1.3.14
@@ -223,7 +224,7 @@ Provides-Extra: dev
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: structlog; extra == "dev"
-Requires-Dist: nomad-docs>=0.1.3; extra == "dev"
+Requires-Dist: nomad-docs>=2.0.1; extra == "dev"
 Requires-Dist: mkdocs; extra == "dev"
 Requires-Dist: mkdocs-material>=9.0; extra == "dev"
 Requires-Dist: pymdown-extensions; extra == "dev"

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/src/nomad_material_processing.egg-info/SOURCES.txt

@@ -57,6 +57,8 @@ src/nomad_material_processing.egg-info/SOURCES.txt
 src/nomad_material_processing.egg-info/dependency_links.txt
 src/nomad_material_processing.egg-info/entry_points.txt
 src/nomad_material_processing.egg-info/requires.txt
+src/nomad_material_processing.egg-info/scm_file_list.json
+src/nomad_material_processing.egg-info/scm_version.json
 src/nomad_material_processing.egg-info/top_level.txt
 src/nomad_material_processing/solution/__init__.py
 src/nomad_material_processing/solution/general.py
@@ -75,6 +77,7 @@ src/nomad_material_processing/vapor_deposition/pvd/thermal.py
 tests/conftest.py
 tests/test_schema.py
 tests/data/test_crystal_growth.archive.yaml
+tests/data/test_crystalline_substrate.archive.yaml
 tests/data/test_czochralski_process.archive.yaml
 tests/data/test_epitaxy.archive.yaml
 tests/data/test_metal_organic_vapor_phase_epitaxy.archive.yaml

{nomad_material_processing-1.0.6 → nomad_material_processing-1.0.7}/src/nomad_material_processing.egg-info/requires.txt

@@ -4,7 +4,7 @@ nomad-lab>=1.3.14
 pytest
 ruff
 structlog
-nomad-docs>=0.1.3
+nomad-docs>=2.0.1
 mkdocs
 mkdocs-material>=9.0
 pymdown-extensions

nomad_material_processing-1.0.7/src/nomad_material_processing.egg-info/scm_file_list.json

@@ -0,0 +1,92 @@
+{
+  "files": [
+    ".github/workflows/mkdocs-deploy.yml",
+    ".github/workflows/python-publish.yml",
+    ".github/workflows/python-test.yml",
+    ".gitignore",
+    ".vscode/settings.json",
+    "CITATION.cff",
+    "LICENSE",
+    "README.md",
+    "docs/assets/.gitignore",
+    "docs/assets/favicon.png",
+    "docs/assets/levelsschema.png",
+    "docs/assets/nomad-logo.png",
+    "docs/assets/nomad-plugin-logo.png",
+    "docs/assets/use-built-in-schema-1.png",
+    "docs/assets/use-built-in-schema-2.png",
+    "docs/contact.md",
+    "docs/explanation/data_model.md",
+    "docs/explanation/levelsofschema.md",
+    "docs/explanation/schemas.md",
+    "docs/how_to/develop.md",
+    "docs/how_to/install.md",
+    "docs/how_to/use_this_plugin.md",
+    "docs/how_to/use_this_plugin_old.md",
+    "docs/index.md",
+    "docs/main.py",
+    "docs/reference/references.md",
+    "docs/reference/schemas.md",
+    "docs/reference/schemas/combinatorial.md",
+    "docs/reference/schemas/crystal_growth.md",
+    "docs/reference/schemas/epitaxy.md",
+    "docs/reference/schemas/general.md",
+    "docs/reference/schemas/solution/general.md",
+    "docs/reference/schemas/vapor_deposition/cvd/general.md",
+    "docs/reference/schemas/vapor_deposition/cvd/movpe.md",
+    "docs/reference/schemas/vapor_deposition/general.md",
+    "docs/reference/schemas/vapor_deposition/pvd/general.md",
+    "docs/reference/schemas/vapor_deposition/pvd/mbe.md",
+    "docs/reference/schemas/vapor_deposition/pvd/pld.md",
+    "docs/reference/schemas/vapor_deposition/pvd/sputtering.md",
+    "docs/reference/schemas/vapor_deposition/pvd/thermal.md",
+    "docs/reference/solution.md",
+    "docs/reference/vapor_depostion.md",
+    "docs/stylesheets/extra.css",
+    "docs/theme/partials/header.html",
+    "docs/tutorial/tutorial.md",
+    "mkdocs.yml",
+    "pyproject.toml",
+    "setup.py",
+    "src/nomad_material_processing/__init__.py",
+    "src/nomad_material_processing/combinatorial.py",
+    "src/nomad_material_processing/crystal_growth.py",
+    "src/nomad_material_processing/epitaxy.py",
+    "src/nomad_material_processing/general.py",
+    "src/nomad_material_processing/solution/__init__.py",
+    "src/nomad_material_processing/solution/general.py",
+    "src/nomad_material_processing/solution/utils.py",
+    "src/nomad_material_processing/utils.py",
+    "src/nomad_material_processing/vapor_deposition/__init__.py",
+    "src/nomad_material_processing/vapor_deposition/cvd/__init__.py",
+    "src/nomad_material_processing/vapor_deposition/cvd/general.py",
+    "src/nomad_material_processing/vapor_deposition/cvd/movpe.py",
+    "src/nomad_material_processing/vapor_deposition/general.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/__init__.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/general.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/mbe.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/pld.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/sputtering.py",
+    "src/nomad_material_processing/vapor_deposition/pvd/thermal.py",
+    "tests/conftest.py",
+    "tests/data/test_crystal_growth.archive.yaml",
+    "tests/data/test_crystalline_substrate.archive.yaml",
+    "tests/data/test_czochralski_process.archive.yaml",
+    "tests/data/test_epitaxy.archive.yaml",
+    "tests/data/test_metal_organic_vapor_phase_epitaxy.archive.yaml",
+    "tests/data/test_molecular_beam_epitaxy.archive.yaml",
+    "tests/data/test_physical_vapor_deposition.archive.yaml",
+    "tests/data/test_pulsed_laser_deposition.archive.yaml",
+    "tests/data/test_sample_deposition.archive.yaml",
+    "tests/data/test_solution.archive.yaml",
+    "tests/data/test_solution_component.archive.yaml",
+    "tests/data/test_sputter_deposition.archive.yaml",
+    "tests/data/test_substrate.archive.yaml",
+    "tests/data/test_thermal_evaporation.archive.yaml",
+    "tests/data/test_thin_film.archive.yaml",
+    "tests/data/test_thin_film_stack.archive.yaml",
+    "tests/data/test_vapor_phase_epitaxy.archive.yaml",
+    "tests/solution/test_solution_schema.py",
+    "tests/test_schema.py"
+  ]
+}

nomad_material_processing-1.0.7/src/nomad_material_processing.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.0.7",
+  "distance": 0,
+  "node": "gb89a0d1841215fbc2f6a214a288e87469745d484",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-11-06"
+}

nomad_material_processing-1.0.7/tests/data/test_crystalline_substrate.archive.yaml

@@ -0,0 +1,4 @@
+data:
+  m_def: nomad_material_processing.CrystallineSubstrate
+  crystal_properties:
+    bravais_lattices: Monoclinic Simple

nomad_material_processing-1.0.7/tests/solution/test_solution_schema.py

@@ -0,0 +1,203 @@
+import pytest
+from nomad.client import normalize_all, parse
+from nomad.datamodel.metainfo.basesections import (
+    PubChemPureSubstanceSection,
+    PureSubstanceSection,
+)
+from nomad.units import ureg
+
+from nomad_material_processing.solution.general import (
+    Solution,
+    SolutionComponent,
+    SolutionComponentReference,
+)
+
+
+@pytest.fixture(autouse=True)
+def mock_pubchem(monkeypatch):
+    """Use fixed enrichment data without querying PubChem."""
+    substances = {
+        'Water': (962, 'H2O', 18.010564684),
+        'Sodium Chloride': (5234, 'ClNa', 57.95862196),
+    }
+
+    def normalize_pubchem(section, archive, logger):
+        if section.name not in substances:
+            pytest.fail(f'No mocked PubChem data for {section.name!r}.')
+        cid, formula, molecular_mass = substances[section.name]
+        section.pub_chem_cid = cid
+        section.molecular_formula = formula
+        section.molecular_mass = molecular_mass * ureg('Da')
+
+        # Run the parent normalization as
+        # PubChemPureSubstanceSection inherits from PureSubstanceSection
+        PureSubstanceSection.normalize(section, archive, logger)
+
+    monkeypatch.setattr(PubChemPureSubstanceSection, 'normalize', normalize_pubchem)
+
+
+def test_solution_component():
+    """
+    Test molar concentration calculation for a solution component.
+    Test mass calculation.
+    """
+    archive = parse('tests/data/test_solution_component.archive.yaml')[0]
+    archive.data = SolutionComponent(
+        volume=1.0 * ureg('l'),
+        density=1.0 * ureg('kg/l'),
+        pure_substance=PubChemPureSubstanceSection(
+            name='Water',
+        ),
+    )
+    normalize_all(archive)
+
+    volume = 1 * ureg('liter')
+    archive.data.calculate_molar_concentration(volume)
+
+    assert archive.data.mass.to('kg').magnitude == pytest.approx(1.0, rel=1e-3)
+    assert archive.data.molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(55.523, rel=1e-3)
+
+
+def test_solution():
+    starter_solution_archive = parse('tests/data/test_solution.archive.yaml')[0]
+    water = PubChemPureSubstanceSection(name='Water')
+    salt = PubChemPureSubstanceSection(name='Sodium Chloride')
+    starter_solution = Solution(
+        name='Starter solution',
+        components=[
+            SolutionComponent(
+                volume=0.50 * ureg('l'),
+                density=1.0 * ureg('kg/l'),
+                pure_substance=water,
+            ),
+            SolutionComponent(
+                mass=0.01 * ureg('kg'),
+                pure_substance=salt,
+                component_role='Solute',
+            ),
+        ],
+    )
+    starter_solution_archive.data = starter_solution
+    normalize_all(starter_solution_archive)
+    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 starter_water_concentration.to('mol/l').magnitude == pytest.approx(
+        55.523, rel=1e-3
+    )
+    assert starter_water_amount.to('mol').magnitude == pytest.approx(
+        0.5 * 55.523, rel=1e-3
+    )
+    assert starter_salt_concentration.to('mol/l').magnitude == pytest.approx(
+        0.345, rel=1e-3
+    )
+    assert starter_salt_mass.to('kg').magnitude == pytest.approx(0.01, rel=1e-3)
+
+    ## making the main solution using starter solution
+    main_solution_archive = parse('tests/data/test_solution.archive.yaml')[0]
+
+    # step 1: portioning the starter solution (one fifth)
+    main_solution_archive.data = Solution(
+        name='Diluted Solution',
+        components=[
+            SolutionComponentReference(
+                system=starter_solution,
+                volume=0.1 * ureg('l'),
+            ),
+        ],
+    )
+    normalize_all(main_solution_archive)
+    assert main_solution_archive.data.solvents[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_water_concentration.to('mol/l').magnitude, rel=1e-3
+    )
+    assert main_solution_archive.data.solvents[0].amount_of_substance.to(
+        'mol'
+    ).magnitude == pytest.approx(starter_water_amount.to('mol').magnitude / 5, rel=1e-3)
+    assert main_solution_archive.data.solutes[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_salt_concentration.to('mol/l').magnitude, rel=1e-3
+    )
+    assert main_solution_archive.data.solutes[0].mass.to(
+        'kg'
+    ).magnitude == pytest.approx(starter_salt_mass.to('kg').magnitude / 5, rel=1e-3)
+
+    # step 2: diluting the solution (double the volume of water)
+    main_solution_archive.data = Solution(
+        name='Diluted Solution',
+        components=[
+            SolutionComponentReference(
+                system=starter_solution,
+                volume=0.1 * ureg('l'),
+            ),
+            SolutionComponent(
+                volume=0.1 * ureg('l'),
+                density=1.0 * ureg('kg/l'),
+                pure_substance=water,
+            ),
+        ],
+    )
+    normalize_all(main_solution_archive)
+    assert main_solution_archive.data.solvents[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_water_concentration.to('mol/l').magnitude, rel=1e-3
+    )
+    assert main_solution_archive.data.solvents[0].amount_of_substance.to(
+        'mol'
+    ).magnitude == pytest.approx(
+        (starter_water_amount.to('mol').magnitude / 5) * 2, rel=1e-3
+    )
+    assert main_solution_archive.data.solutes[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_salt_concentration.to('mol/l').magnitude / 2, rel=1e-3
+    )
+    assert main_solution_archive.data.solutes[0].mass.to(
+        'kg'
+    ).magnitude == pytest.approx(starter_salt_mass.to('kg').magnitude / 5, rel=1e-3)
+
+    # finally, quantities in the starter solution should stay the same
+    # after all normalizations
+    assert starter_solution_archive.data.solvents[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_water_concentration.to('mol/l').magnitude, rel=1e-3
+    )
+    assert starter_solution_archive.data.solvents[0].amount_of_substance.to(
+        'mol'
+    ).magnitude == pytest.approx(starter_water_amount.to('mol').magnitude, rel=1e-3)
+    assert starter_solution_archive.data.solutes[
+        0
+    ].molar_concentration.calculated_concentration.to(
+        'mol/l'
+    ).magnitude == pytest.approx(
+        starter_salt_concentration.to('mol/l').magnitude, rel=1e-3
+    )
+    assert starter_solution_archive.data.solutes[0].mass.to(
+        'kg'
+    ).magnitude == pytest.approx(starter_salt_mass.to('kg').magnitude, rel=1e-3)
+
+
+if __name__ == '__main__':
+    test_solution()

nomad_material_processing-1.0.7/tests/test_schema.py

@@ -0,0 +1,29 @@
+import glob
+import os.path
+
+import pytest
+from nomad.client import normalize_all, parse
+
+test_files = glob.glob(
+    os.path.join(os.path.dirname(__file__), 'data', '*.archive.yaml')
+)
+
+
+@pytest.mark.parametrize('test_file', test_files)
+def test_schema(test_file):
+    entry_archive = parse(test_file)[0]
+    normalize_all(entry_archive)
+
+
+def test_crystalline_substrate_bravais_lattice_normalization():
+    test_file = os.path.join(
+        os.path.dirname(__file__),
+        'data',
+        'test_crystalline_substrate.archive.yaml',
+    )
+    entry_archive = parse(test_file)[0]
+    normalize_all(entry_archive)
+
+    assert (
+        entry_archive.data.crystal_properties.bravais_lattices == 'Monoclinic Primitive'
+    )

nomad_material_processing-1.0.6/tests/solution/test_solution_schema.py

@@ -1,198 +0,0 @@
-import pytest
-from nomad.client import normalize_all, parse
-from nomad.datamodel.metainfo.basesections import PubChemPureSubstanceSection
-from nomad.units import ureg
-
-from nomad_material_processing.solution.general import (
-    Solution,
-    SolutionComponent,
-    SolutionComponentReference,
-)
-
-
-def test_solution_component():
-    """
-    Test molar concentration calculation for a solution component.
-    Test mass calculation.
-    """
-    archive = parse('tests/data/test_solution_component.archive.yaml')[0]
-    archive.data = SolutionComponent(
-        volume=1.0 * ureg('l'),
-        density=1.0 * ureg('kg/l'),
-        pure_substance=PubChemPureSubstanceSection(
-            name='Water',
-        ),
-    )
-    normalize_all(archive)
-
-    volume = 1 * ureg('liter')
-    archive.data.calculate_molar_concentration(volume)
-
-    assert pytest.approx(archive.data.mass, 1e-3) == 1.0 * ureg('kg')
-    assert pytest.approx(
-        archive.data.molar_concentration.calculated_concentration, 1e-3
-    ) == 55.523 * ureg('mol/l')
-
-
-def test_solution():
-    starter_solution_archive = parse('tests/data/test_solution.archive.yaml')[0]
-    water = PubChemPureSubstanceSection(name='Water')
-    salt = PubChemPureSubstanceSection(name='Sodium Chloride')
-    starter_solution = Solution(
-        name='Starter solution',
-        components=[
-            SolutionComponent(
-                volume=0.50 * ureg('l'),
-                density=1.0 * ureg('kg/l'),
-                pure_substance=water,
-            ),
-            SolutionComponent(
-                mass=0.01 * ureg('kg'),
-                pure_substance=salt,
-                component_role='Solute',
-            ),
-        ],
-    )
-    starter_solution_archive.data = starter_solution
-    normalize_all(starter_solution_archive)
-    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')
-
-    ## making the main solution using starter solution
-    main_solution_archive = parse('tests/data/test_solution.archive.yaml')[0]
-
-    # step 1: portioning the starter solution (one fifth)
-    main_solution_archive.data = Solution(
-        name='Diluted Solution',
-        components=[
-            SolutionComponentReference(
-                system=starter_solution,
-                volume=0.1 * ureg('l'),
-            ),
-        ],
-    )
-    normalize_all(main_solution_archive)
-    assert (
-        pytest.approx(
-            main_solution_archive.data.solvents[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == 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[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == starter_salt_concentration
-    )
-    assert (
-        pytest.approx(main_solution_archive.data.solutes[0].mass, 1e-3)
-        == starter_salt_mass / 5
-    )
-
-    # step 2: diluting the solution (double the volume of water)
-    main_solution_archive.data = Solution(
-        name='Diluted Solution',
-        components=[
-            SolutionComponentReference(
-                system=starter_solution,
-                volume=0.1 * ureg('l'),
-            ),
-            SolutionComponent(
-                volume=0.1 * ureg('l'),
-                density=1.0 * ureg('kg/l'),
-                pure_substance=water,
-            ),
-        ],
-    )
-    normalize_all(main_solution_archive)
-    assert (
-        pytest.approx(
-            main_solution_archive.data.solvents[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == 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[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == starter_salt_concentration / 2
-    )
-    assert (
-        pytest.approx(main_solution_archive.data.solutes[0].mass, 1e-3)
-        == starter_salt_mass / 5
-    )
-
-    # finally, quantities in the starter solution should stay the same
-    # after all normalizations
-    assert (
-        pytest.approx(
-            starter_solution_archive.data.solvents[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == 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[
-                0
-            ].molar_concentration.calculated_concentration,
-            1e-3,
-        )
-        == starter_salt_concentration
-    )
-    assert (
-        pytest.approx(starter_solution_archive.data.solutes[0].mass, 1e-3)
-        == starter_salt_mass
-    )
-
-
-if __name__ == '__main__':
-    test_solution()

nomad_material_processing-1.0.6/tests/test_schema.py

@@ -1,15 +0,0 @@
-import glob
-import os.path
-
-import pytest
-from nomad.client import normalize_all, parse
-
-test_files = glob.glob(
-    os.path.join(os.path.dirname(__file__), 'data', '*.archive.yaml')
-)
-
-
-@pytest.mark.parametrize('test_file', test_files)
-def test_schema(test_file):
-    entry_archive = parse(test_file)[0]
-    normalize_all(entry_archive)