From 9b4c86e631df6a9ab5c07afc72b6cd40f5027657 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Fri, 6 Sep 2024 19:08:15 -0700
Subject: [PATCH] feat: first implementation of slab grain boundary

---
 .../tools/build/grain_boundary/__init__.py    | 92 ++++++++++++++++++-
 1 file changed, 91 insertions(+), 1 deletion(-)

diff --git a/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py b/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py
index 8898def1..e184ace0 100644
--- a/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py
+++ b/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py
@@ -1,6 +1,14 @@
+from numpy.ma.setup import configuration
 from pydantic import BaseModel
+from mat3ra.made.material import Material
 from mat3ra.code.entity import InMemoryEntity
-from ..slab import SlabConfiguration, Termination
+
+from .. import BaseBuilder
+from ..interface import ZSLStrainMatchingInterfaceBuilderParameters, InterfaceConfiguration
+from ..supercell import create_supercell
+from ...analyze import get_chemical_formula
+from ..interface.builders import InterfaceBuilder, ZSLStrainMatchingInterfaceBuilder
+from ..slab import SlabConfiguration, Termination, get_terminations, SlabBuilder, SlabSelectorParameters
 
 
 class GrainBoundaryConfiguration(BaseModel, InMemoryEntity):
@@ -10,6 +18,7 @@ class GrainBoundaryConfiguration(BaseModel, InMemoryEntity):
     phase_2_termination: Termination
     gap: float = 3.0
     slab_configuration: SlabConfiguration
+    slab_termination: Termination
 
     @property
     def _json(self):
@@ -22,3 +31,84 @@ def _json(self):
             "gap": self.gap,
             "slab_configuration": self.slab_configuration.to_json(),
         }
+
+
+class GrainBoundaryBuilderParameters(ZSLStrainMatchingInterfaceBuilderParameters):
+    selected_interface_index: int = 0
+
+
+class GrainBoundaryBuilder(BaseBuilder):
+    _BuildParametersType = GrainBoundaryBuilderParameters
+    _ConfigurationType: type(GrainBoundaryConfiguration) = GrainBoundaryConfiguration  # type: ignore
+
+    def _generate(self, configuration: GrainBoundaryConfiguration):
+        interface = self._create_interface(configuration)
+        rotated_interface = create_supercell(interface, [[0, 0, 1], [0, 1, 0], [-1, 0, 0]])
+        slab_config = SlabConfiguration(
+            bulk=rotated_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),
+        )
+
+        return [final_slab]
+
+    def _create_interface(self, configuration: GrainBoundaryConfiguration):
+        phase_1_config = configuration.phase_1_configuration
+        phase_2_config = configuration.phase_2_configuration
+        phase_1_termination = (
+            configuration.phase_1_termination
+            if configuration.phase_1_termination
+            else get_terminations(phase_1_config)[0]
+        )
+        phase_2_termination = (
+            configuration.phase_2_termination
+            if configuration.phase_2_termination
+            else get_terminations(phase_2_config)[0]
+        )
+
+        interface_configuration = InterfaceConfiguration(
+            film_configuration=phase_1_config,
+            substrate_configuration=phase_2_config,
+            film_termination=phase_1_termination,
+            substrate_termination=phase_2_termination,
+            distance_z=configuration.gap,
+            vacuum=configuration.gap,
+        )
+
+        zsl_parameters = self.build_parameters
+        matched_interfaces_builder = ZSLStrainMatchingInterfaceBuilder(
+            build_parameters=ZSLStrainMatchingInterfaceBuilderParameters(strain_matching_parameters=zsl_parameters)
+        )
+
+        interfaces_sorted_by_size_and_strain = matched_interfaces_builder.get_materials(
+            configuration=interface_configuration
+        )
+
+        selected_interface = interfaces_sorted_by_size_and_strain[self.build_parameters.selected_interface_index]
+        return selected_interface
+
+    def _create_slab(self, configuration: GrainBoundaryConfiguration):
+        pass
+
+    def _update_material_name(self, material: Material, configuration: GrainBoundaryConfiguration) -> 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