From 9723057b2e16102dc26446bf9b69fe9d870cf5ab Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 24 Sep 2024 19:34:38 -0700
Subject: [PATCH] update: make work

---
 .../tools/build/grain_boundary/__init__.py    | 41 ++++++++++---------
 .../tools/build/interface/configuration.py    |  6 ++-
 2 files changed, 25 insertions(+), 22 deletions(-)

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 75a674e0..69396acd 100644
--- a/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py
+++ b/src/py/mat3ra/made/tools/build/grain_boundary/__init__.py
@@ -7,47 +7,48 @@
 from mat3ra.made.tools.build.interface.builders import CommensurateLatticeTwistedInterfaceBuilder
 from mat3ra.made.tools.build.supercell import create_supercell
 from mat3ra.made.tools.build.utils import merge_materials
-from mat3ra.made.tools.modify import translate_by_vector, filter_by_box
+from mat3ra.made.tools.modify import filter_by_box
 
 
-class SurfaceGrainBoundaryConfiguration(BaseConfiguration):
+from mat3ra.made.tools.build.interface.configuration import TwistedInterfaceConfiguration
+
+
+class SurfaceGrainBoundaryConfiguration(TwistedInterfaceConfiguration):
     """
     Configuration for creating a surface grain boundary.
 
     Args:
-        material (Material): The material to create two phases of the grain boundary.
-        angle (float): The angle between the orientations of the two phases.
         gap (float): The gap between the two phases.
     """
 
-    material: Material
-    angle: float = 0.0
     gap: float = 0.0
 
     @property
     def _json(self):
         return {
             "type": self.get_cls_name(),
-            "material": self.material.to_json(),
-            "angle": self.angle,
+            "gap": self.gap,
         }
 
 
 class SurfaceGrainBoundaryBuilder(CommensurateLatticeTwistedInterfaceBuilder):
-    def _post_process(
-        self,
-        items: List[CommensurateLatticeTwistedInterfaceBuilder._GeneratedItemType],
-        post_process_parameters=None,
-    ) -> List[Material]:
-        grain_boundary_materials = []
+    _ConfigurationType: type(SurfaceGrainBoundaryConfiguration) = SurfaceGrainBoundaryConfiguration  # type: ignore
+
+    def _post_process(self, items: List[Material], post_process_parameters=None) -> List[Material]:
+        grain_boundaries = []
         for item in items:
             phase_1_material_initial = create_supercell(item.configuration.film, item.matrix1.tolist())
-            phase_1_material_doubled = create_supercell(phase_1_material_initial, scaling_factors=[2, 1, 1])
+            phase_1_material_doubled = create_supercell(phase_1_material_initial, scaling_factor=[2, 1, 1])
             phase_1_material = filter_by_box(phase_1_material_doubled, [0, 0, 0], [0.5, 1, 1])
-            phase_2_material_initial = create_supercell(item.configuration.substrate, item.matrix2.tolist())
-            phase_2_material_doubled = create_supercell(phase_2_material_initial, scaling_factors=[2, 1, 1])
+            phase_2_material_initial = create_supercell(item.configuration.film, item.matrix2.tolist())
+            phase_2_material_doubled = create_supercell(phase_2_material_initial, scaling_factor=[2, 1, 1])
             phase_2_material = filter_by_box(phase_2_material_doubled, [0.5, 0, 0], [1, 1, 1])
+
             interface = merge_materials([phase_1_material, phase_2_material])
-            interface.metadata["actual_twist_angle"] = item.angle
-            grain_boundary_materials.append(interface)
-        return grain_boundary_materials
+            grain_boundaries.append(interface)
+
+        return grain_boundaries
+
+    def _update_material_name(self, material: Material, configuration: SurfaceGrainBoundaryConfiguration) -> Material:
+        material.name = f"Surface Grain Boundary ({configuration.twist_angle:.2f}°)"
+        return material
diff --git a/src/py/mat3ra/made/tools/build/interface/configuration.py b/src/py/mat3ra/made/tools/build/interface/configuration.py
index 8d29f827..5269c7aa 100644
--- a/src/py/mat3ra/made/tools/build/interface/configuration.py
+++ b/src/py/mat3ra/made/tools/build/interface/configuration.py
@@ -1,3 +1,5 @@
+from typing import Optional
+
 from mat3ra.code.entity import InMemoryEntity
 from pydantic import BaseModel
 
@@ -35,7 +37,7 @@ def _json(self):
 
 class TwistedInterfaceConfiguration(BaseConfiguration):
     film: Material
-    substrate: Material
+    substrate: Optional[Material] = None
     twist_angle: float = 0.0
     distance_z: float = 3.0
 
@@ -44,7 +46,7 @@ def _json(self):
         return {
             "type": self.get_cls_name(),
             "film": self.film.to_json(),
-            "substrate": self.substrate.to_json(),
+            "substrate": self.substrate.to_json() if self.substrate else None,
             "twist_angle": self.twist_angle,
             "distance_z": self.distance_z,
         }