feature/SOF-7433 feat: add grain boundary

src/py/mat3ra/made/tools/build/__init__.py

@@ -23,6 +23,15 @@ def _json(self):
         raise NotImplementedError
 
 
+class BaseSelectorParameters(BaseModel):
+    default_index: int = 0
+
+
+class BaseBuilderParameters(BaseModel):
+    class Config:
+        arbitrary_types_allowed = True
+
+
 class BaseBuilder(BaseModel):
     """
     Base class for material builders.
@@ -56,6 +65,7 @@ class BaseBuilder(BaseModel):
     _GeneratedItemType: Any = Any
     _SelectorParametersType: Any = None
     _PostProcessParametersType: Any = None
+    selector_parameters: Any = BaseSelectorParameters()
 
     def __init__(self, build_parameters: _BuildParametersType = None):
         super().__init__(build_parameters=build_parameters)
@@ -115,7 +125,9 @@ def get_material(
         selector_parameters: Optional[_SelectorParametersType] = None,
         post_process_parameters: Optional[_PostProcessParametersType] = None,
     ) -> Material:
-        return self.get_materials(configuration, selector_parameters, post_process_parameters)[0]
+        return self.get_materials(configuration, selector_parameters, post_process_parameters)[
+            self.selector_parameters.default_index
+        ]
 
     def _update_material_name(self, material, configuration):
         # Do nothing by default

src/py/mat3ra/made/tools/build/grain_boundary/__init__.py

@@ -0,0 +1,15 @@
+from typing import Optional
+
+from mat3ra.made.material import Material
+
+from .builders import GrainBoundaryBuilder
+from .configuration import GrainBoundaryConfiguration
+
+
+def create_grain_boundary(
+    configuration: GrainBoundaryConfiguration,
+    builder: Optional[GrainBoundaryBuilder] = None,
+) -> Material:
+    if builder is None:
+        builder = GrainBoundaryBuilder()
+    return builder.get_material(configuration)

src/py/mat3ra/made/tools/build/grain_boundary/builders.py

@@ -0,0 +1,84 @@
+from typing import List
+
+from mat3ra.made.material import Material
+
+from ...analyze import get_chemical_formula
+from ..interface import ZSLStrainMatchingInterfaceBuilderParameters, InterfaceConfiguration
+from ..interface.builders import ZSLStrainMatchingInterfaceBuilder
+from ..supercell import create_supercell
+from ..slab import SlabConfiguration, get_terminations, SlabBuilder, SlabSelectorParameters
+from .configuration import GrainBoundaryConfiguration
+
+
+class GrainBoundaryBuilderParameters(ZSLStrainMatchingInterfaceBuilderParameters):
+    selected_interface_index: int = 0
+
+
+class GrainBoundaryBuilder(ZSLStrainMatchingInterfaceBuilder):
+    """
+    A builder for creating grain boundaries.
+
+    The grain boundary is created by:
+    1. creating an interface between two phases,
+    2. then rotating the interface by 90 degrees.
+    3. Finally, creating a slab from the rotated interface.
+    """
+
+    _BuildParametersType: type(GrainBoundaryBuilderParameters) = GrainBoundaryBuilderParameters  # type: ignore
+    _ConfigurationType: type(GrainBoundaryConfiguration) = GrainBoundaryConfiguration  # type: ignore
+    _GeneratedItemType: type(Material) = Material  # type: ignore
+    selector_parameters: type(  # type: ignore
+        GrainBoundaryBuilderParameters
+    ) = GrainBoundaryBuilderParameters().selected_interface_index  # type: ignore
+
+    def _generate(self, configuration: _ConfigurationType) -> List[Material]:
+        interface_config = InterfaceConfiguration(
+            film_configuration=configuration.phase_1_configuration,
+            substrate_configuration=configuration.phase_2_configuration,
+            film_termination=configuration.phase_1_termination,
+            substrate_termination=configuration.phase_2_termination,
+            distance_z=configuration.gap,
+            vacuum=configuration.gap,
+        )
+        interfaces = super()._generate(interface_config)
+        rot_90_degree_matrix = [[0, 1, 0], [-1, 0, 0], [0, 0, 1]]
+        rotated_interfaces = [
+            create_supercell(interface, xy_supercell_matrix=rot_90_degree_matrix) for interface in interfaces
+        ]
+        return rotated_interfaces
+
+    def _finalize(self, materials: List[Material], configuration: _ConfigurationType) -> List[Material]:
+        final_slabs = []
+        for interface in materials:
+            slab_config = SlabConfiguration(
+                bulk=interface,
+                miller_indices=configuration.slab_configuration.miller_indices,
+                thickness=configuration.slab_configuration.thickness,
+                vacuum=configuration.slab_configuration.vacuum,
+                xy_supercell_matrix=configuration.slab_configuration.xy_supercell_matrix,
+                use_conventional_cell=True,
+                use_orthogonal_z=True,
+            )
+            slab_builder = SlabBuilder()
+            slab_termination = (
+                configuration.slab_termination if configuration.slab_termination else get_terminations(slab_config)[0]
+            )
+            final_slab = slab_builder.get_material(
+                configuration,
+                selector_parameters=SlabSelectorParameters(termination=slab_termination),
+            )
+            final_slabs.append(final_slab)
+
+        materials = super()._finalize(final_slabs, configuration)
+        return materials
+
+    def _update_material_name(self, material: Material, configuration: _ConfigurationType) -> Material:
+        phase_1_formula = get_chemical_formula(configuration.phase_1_configuration.bulk)
+        phase_2_formula = get_chemical_formula(configuration.phase_2_configuration.bulk)
+        phase_1_miller_indices = "".join([str(i) for i in configuration.phase_1_configuration.miller_indices])
+        phase_2_miller_indices = "".join([str(i) for i in configuration.phase_2_configuration.miller_indices])
+        new_name = (
+            f"{phase_1_formula}({phase_1_miller_indices})-{phase_2_formula}({phase_2_miller_indices}), Grain Boundary"
+        )
+        material.name = new_name
+        return material

src/py/mat3ra/made/tools/build/grain_boundary/configuration.py

@@ -0,0 +1,41 @@
+from typing import Optional
+
+from .. import BaseConfiguration
+from ..slab.configuration import SlabConfiguration
+from ..slab.termination import Termination
+
+
+class GrainBoundaryConfiguration(BaseConfiguration):
+    """
+    Configuration for a grain boundary in a slab material.
+
+    Attributes:
+        phase_1_configuration: SlabConfiguration
+        phase_2_configuration: SlabConfiguration
+        phase_1_termination: Termination
+        phase_2_termination: Termination
+        gap: float
+        slab_configuration: SlabConfiguration
+        slab_termination: Termination
+
+    """
+
+    phase_1_configuration: SlabConfiguration
+    phase_2_configuration: SlabConfiguration
+    phase_1_termination: Termination
+    phase_2_termination: Termination
+    gap: float = 3.0
+    slab_configuration: SlabConfiguration
+    slab_termination: Optional[Termination]
+
+    @property
+    def _json(self):
+        return {
+            "type": "GrainBoundaryConfiguration",
+            "phase_1_configuration": self.phase_1_configuration.to_json(),
+            "phase_2_configuration": self.phase_2_configuration.to_json(),
+            "phase_1_termination": str(self.phase_1_termination),
+            "phase_2_termination": str(self.phase_2_termination),
+            "gap": self.gap,
+            "slab_configuration": self.slab_configuration.to_json(),
+        }

src/py/mat3ra/made/tools/build/interface/builders.py

@@ -22,7 +22,7 @@
 from ..slab.configuration import SlabConfiguration
 from ...analyze import get_chemical_formula
 from ...convert import to_ase, from_ase, to_pymatgen, PymatgenInterface, ASEAtoms
-from ...build import BaseBuilder
+from ...build import BaseBuilder, BaseBuilderParameters
 
 
 class InterfaceBuilderParameters(BaseModel):
@@ -106,7 +106,7 @@ def _post_process(self, items: List[_GeneratedItemType], post_process_parameters
 ########################################################################################
 #                       Strain Matching Interface Builders                             #
 ########################################################################################
-class StrainMatchingInterfaceBuilderParameters(BaseModel):
+class StrainMatchingInterfaceBuilderParameters(BaseBuilderParameters):
     strain_matching_parameters: Optional[Any] = None
 
 
@@ -130,7 +130,7 @@ class ZSLStrainMatchingParameters(BaseModel):
 
 
 class ZSLStrainMatchingInterfaceBuilderParameters(StrainMatchingInterfaceBuilderParameters):
-    strain_matching_parameters: ZSLStrainMatchingParameters
+    strain_matching_parameters: ZSLStrainMatchingParameters = ZSLStrainMatchingParameters()
 
 
 class ZSLStrainMatchingInterfaceBuilder(ConvertGeneratedItemsPymatgenStructureMixin, StrainMatchingInterfaceBuilder):

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

@@ -1,16 +1,15 @@
 from typing import List, Tuple, Any
 
 import numpy as np
-from pydantic import BaseModel
-
-from mat3ra.code.entity import InMemoryEntity
 
 from mat3ra.made.material import Material
+
+from .. import BaseConfiguration
 from ...third_party import PymatgenSpacegroupAnalyzer
 from ...convert import to_pymatgen, from_pymatgen
 
 
-class SlabConfiguration(BaseModel, InMemoryEntity):
+class SlabConfiguration(BaseConfiguration):
     """
     Configuration for building a slab.