feature/SOF-8034 Fix: preserve the input crystal in build metadata

src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/helpers.py

@@ -10,7 +10,6 @@
     SlabStrainedSupercellConfiguration,
 )
 from ......analyze.interface import CommensurateLatticeInterfaceAnalyzer
-from ......analyze.lattice import get_material_with_conventional_lattice
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from ......build_components.metadata import MaterialWithBuildMetadata
 
@@ -53,9 +52,6 @@ def get_commensurate_strained_configurations(
     Raises:
         ValueError: If no commensurate lattice matches are found.
     """
-    if use_conventional_cell:
-        material = get_material_with_conventional_lattice(material)
-
     slab_config = SlabConfiguration.from_parameters(
         material_or_dict=material,
         miller_indices=miller_indices,

src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/zsl/helpers.py

@@ -4,7 +4,6 @@
 
 from mat3ra.made.material import Material
 from ......analyze.interface import ZSLInterfaceAnalyzer
-from ......analyze.lattice import get_material_with_conventional_lattice
 from ......analyze.slab import SlabMaterialAnalyzer
 from ......build.compound_pristine_structures.two_dimensional.interface import (
     InterfaceBuilderParameters,
@@ -37,10 +36,6 @@ def create_interface_zsl(
     reduce_result_cell: bool = True,
     reduce_result_cell_to_primitive: bool = False,
 ) -> MaterialWithBuildMetadata:
-    if use_conventional_cell:
-        substrate_crystal = get_material_with_conventional_lattice(substrate_crystal)
-        film_crystal = get_material_with_conventional_lattice(film_crystal)
-
     substrate_slab = create_slab(
         crystal=substrate_crystal,
         miller_indices=substrate_miller_indices,

src/py/mat3ra/made/tools/build/defective_structures/one_dimensional/grain_boundary_linear/helpers.py

@@ -7,7 +7,6 @@
 from .builder import GrainBoundaryLinearBuilder
 from .configuration import GrainBoundaryLinearConfiguration
 from ....compound_pristine_structures.two_dimensional.interface import get_commensurate_strained_configurations
-from .....analyze.lattice import get_material_with_conventional_lattice
 from .....build_components import MaterialWithBuildMetadata
 
 
@@ -53,9 +52,6 @@ def create_grain_boundary_linear(
     Raises:
         ValueError: If no commensurate lattice matches are found.
     """
-    if use_conventional_cell:
-        material = get_material_with_conventional_lattice(material)
-
     strained_configs, actual_angle = get_commensurate_strained_configurations(
         material=material,
         target_angle=target_angle,

src/py/mat3ra/made/tools/build/defective_structures/two_dimensional/grain_boundary_planar/helpers.py

@@ -4,7 +4,6 @@
 from .builder import GrainBoundaryPlanarBuilder
 from .configuration import GrainBoundaryPlanarConfiguration
 from .....analyze.interface import GrainBoundaryPlanarAnalyzer
-from .....analyze.lattice import get_material_with_conventional_lattice
 from .....build_components import MaterialWithBuildMetadata
 
 
@@ -45,10 +44,6 @@ def create_grain_boundary_planar(
         Material: The grain boundary material
     """
     phase_2_material = phase_2_material or phase_1_material
-    if use_conventional_cell:
-        phase_1_material = get_material_with_conventional_lattice(phase_1_material)
-        phase_2_material = get_material_with_conventional_lattice(phase_2_material)
-
     analyzer = GrainBoundaryPlanarAnalyzer(
         phase_1_material=phase_1_material,
         phase_2_material=phase_2_material,

src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py

@@ -81,11 +81,10 @@ def from_parameters(
         termination_top = select_slab_termination(terminations, termination_top_formula)
         termination_bottom = select_slab_termination(terminations, termination_bottom_formula)
 
-        if use_conventional_cell:
-            material = crystal_lattice_planes_analyzer.material_with_conventional_lattice
         atomic_layers_repeated_configuration = AtomicLayersUniqueRepeatedConfiguration(
             crystal=material,
             miller_indices=miller_indices,
+            use_conventional_cell=use_conventional_cell,
             termination_top=termination_top,
             termination_bottom=termination_bottom,
             number_of_repetitions=number_of_layers,

src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/helpers.py

@@ -32,6 +32,7 @@ def create_atomic_layers(
     atomic_layers_config = AtomicLayersUniqueRepeatedConfiguration(
         crystal=material,
         miller_indices=miller_indices,
+        use_conventional_cell=False,
         termination_top=termination,
         number_of_repetitions=number_of_layers,
     )

src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/crystal_lattice_planes/builder.py

@@ -21,7 +21,10 @@ def get_analyzer(self, configuration: CrystalLatticePlanesConfiguration) -> Crys
     def _generate(self, configuration: CrystalLatticePlanesConfiguration) -> MaterialWithBuildMetadata:
         crystal_lattice_planes_analyzer = self.get_analyzer(configuration)
         miller_supercell_matrix = crystal_lattice_planes_analyzer.miller_supercell_matrix
-        miller_supercell_material = supercell(configuration.crystal, miller_supercell_matrix)
+        crystal = configuration.crystal
+        if configuration.use_conventional_cell:
+            crystal = crystal_lattice_planes_analyzer.material_with_conventional_lattice
+        miller_supercell_material = supercell(crystal, miller_supercell_matrix)
         return miller_supercell_material
 
     def _enforce_convention(self, material: MaterialWithBuildMetadata) -> MaterialWithBuildMetadata:

tests/py/unit/fixtures/slab.py

@@ -604,3 +604,25 @@
         "type": "TRI",
     },
 }
+
+
+ATOMIC_LAYERS_NI_001: Dict[str, Any] = {
+    "name": "Ni(001), termination Ni_P4/mmm_2",
+    "basis": {
+        "elements": [{"id": 0, "value": "Ni"}],
+        "coordinates": [{"id": 0, "value": [0.0, 0.0, 1e-06]}],
+        "units": "crystal",
+        "labels": [],
+        "constraints": [],
+    },
+    "lattice": {
+        "a": 2.478974,
+        "b": 2.478974,
+        "c": 2.478974,
+        "alpha": 60.0,
+        "beta": 60.0,
+        "gamma": 60.0,
+        "units": {"length": "angstrom", "angle": "degree"},
+        "type": "TRI",
+    },
+}

tests/py/unit/test_build_metadata_records_input_crystal.py

@@ -0,0 +1,93 @@
+from typing import Any, Dict, List
+
+import pytest
+from mat3ra.made.material import Material
+from mat3ra.made.tools.helpers import (
+    create_atomic_layers,
+    create_defect_point_vacancy,
+    create_grain_boundary_linear,
+    create_grain_boundary_planar,
+    create_interface_commensurate,
+    create_interface_twisted,
+    create_interface_zsl,
+    create_slab,
+    get_slab_terminations,
+)
+
+from .fixtures.bulk import BULK_Ni_PRIMITIVE
+from .fixtures.slab import ATOMIC_LAYERS_NI_001
+from .utils import assert_two_entities_deep_almost_equal
+
+MILLER_INDICES = (0, 0, 1)
+BULK_Ni_PRIMITIVE_WITH_ID: Dict[str, Any] = {**BULK_Ni_PRIMITIVE, "_id": "platform-id-abc"}
+
+BUILDERS = {
+    "slab": lambda crystal: create_slab(crystal=crystal, miller_indices=MILLER_INDICES, number_of_layers=3),
+    "interface_zsl": lambda crystal: create_interface_zsl(
+        substrate_crystal=crystal, film_crystal=crystal, max_area=50.0
+    ),
+    "interface_commensurate": lambda crystal: create_interface_commensurate(
+        material=crystal, target_angle=13.0, angle_tolerance=0.5, max_repetition_int=5
+    ),
+    "grain_boundary_planar": lambda crystal: create_grain_boundary_planar(
+        phase_1_material=crystal,
+        phase_1_miller_indices=MILLER_INDICES,
+        phase_2_miller_indices=(0, 1, 1),
+        max_area=100.0,
+    ),
+    "grain_boundary_linear": lambda crystal: create_grain_boundary_linear(
+        material=crystal, target_angle=13.0, angle_tolerance=0.5, max_repetition_int=5, gap=1.0
+    ),
+    "point_defect_vacancy": lambda crystal: create_defect_point_vacancy(crystal, [0.0, 0.0, 0.0], "closest_site"),
+}
+
+
+def get_recorded_source_crystals(node: Any) -> List[Dict[str, Any]]:
+    """Crystals recorded next to Miller indices, plus defect hosts. A vacuum's is a built intermediate."""
+    if isinstance(node, list):
+        return [crystal for item in node for crystal in get_recorded_source_crystals(item)]
+    if not isinstance(node, dict):
+        return []
+    crystals = []
+    collected = set()
+    if isinstance(node.get("crystal"), dict) and "miller_indices" in node:
+        crystals.append(node["crystal"])
+        collected.add("crystal")
+    if node.get("merge_components"):
+        crystals.append(node["merge_components"][0])
+        collected.add("merge_components")
+    return crystals + [
+        found for key, value in node.items() if key not in collected for found in get_recorded_source_crystals(value)
+    ]
+
+
+@pytest.mark.parametrize("build", BUILDERS.values(), ids=BUILDERS.keys())
+def test_recorded_crystal_is_the_input(build):
+    material = Material.create(BULK_Ni_PRIMITIVE_WITH_ID)
+
+    built = build(material)
+
+    recorded = get_recorded_source_crystals(built.model_dump()["metadata"]["build"])
+    assert recorded
+    for crystal in recorded:
+        assert_two_entities_deep_almost_equal(crystal, material)
+
+
+@pytest.mark.parametrize("material_config, expected_number_of_atoms, expected_gamma", [(BULK_Ni_PRIMITIVE, 8, 90.0)])
+def test_create_interface_twisted_uses_conventional_cell(material_config, expected_number_of_atoms, expected_gamma):
+    crystal = Material.create(material_config)
+
+    interface = create_interface_twisted(material1=crystal, material2=crystal, angle=10.0, use_conventional_cell=True)
+
+    assert len(interface.basis.elements.values) == expected_number_of_atoms
+    assert interface.lattice.gamma == pytest.approx(expected_gamma)
+
+
+@pytest.mark.parametrize("material_config, expected_material_config", [(BULK_Ni_PRIMITIVE, ATOMIC_LAYERS_NI_001)])
+def test_create_atomic_layers(material_config, expected_material_config):
+    material = Material.create(material_config)
+    termination = get_slab_terminations(material, MILLER_INDICES)[0]
+
+    atomic_layers = create_atomic_layers(material, MILLER_INDICES, termination=termination)
+
+    assert_two_entities_deep_almost_equal(atomic_layers, expected_material_config)

tests/py/unit/test_tools_build_interface.py

@@ -5,7 +5,6 @@
 from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
 from mat3ra.made.material import Material
 from mat3ra.made.tools.analyze.interface.simple import InterfaceAnalyzer
-from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
 from mat3ra.made.tools.build import MaterialWithBuildMetadata
 from mat3ra.made.tools.build.compound_pristine_structures.two_dimensional.interface.base.build_parameters import (
     InterfaceBuilderParameters,
@@ -259,9 +258,6 @@ def test_commensurate_interface_creation(material_config, analyzer_params, direc
 def test_create_slab_with_conventional_cell_stores_crystal_hashes_in_metadata():
     miller_indices = (0, 0, 1)
     material = Material.create(BULK_Ni_PRIMITIVE)
-    expected_crystal = CrystalLatticePlanesMaterialAnalyzer(
-        material=material, miller_indices=miller_indices
-    ).material_with_conventional_lattice
 
     slab = create_slab(
         crystal=material,
@@ -274,8 +270,8 @@ def test_create_slab_with_conventional_cell_stores_crystal_hashes_in_metadata():
     serialized_slab = slab.model_dump()
     crystal = serialized_slab["metadata"]["build"][-1]["configuration"]["stack_components"][0]["crystal"]
 
-    assert crystal[HASH_KEY] == expected_crystal.hash
-    assert crystal[SCALED_HASH_KEY] == expected_crystal.scaled_hash
+    assert crystal[HASH_KEY] == material.hash
+    assert crystal[SCALED_HASH_KEY] == material.scaled_hash
     assert "bulkId" not in serialized_slab["metadata"]
 
 

tests/py/unit/test_tools_build_slab.py

@@ -144,6 +144,7 @@ def get_slab_with_builder(
     atomic_layers_repeated_configuration = AtomicLayersUniqueRepeatedConfiguration(
         crystal=material,
         miller_indices=miller_indices,
+        use_conventional_cell=False,
         termination_top=termination_top,
         termination_bottom=termination_bottom,
         number_of_repetitions=number_of_layers,