update: restrucutre gb directory

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

@@ -1,73 +1,2 @@
-from typing import List
-
-import numpy as np
-
-from mat3ra.made.material import Material
-
-from ..interface.configuration import TwistedInterfaceConfiguration
-from ..interface.builders import (
-    CommensurateLatticeTwistedInterfaceBuilder,
-    CommensurateLatticeTwistedInterfaceBuilderParameters,
-)
-from ..supercell import create_supercell
-from ..utils import merge_two_materials_laterally
-
-
-class SurfaceGrainBoundaryConfiguration(TwistedInterfaceConfiguration):
-    """
-    Configuration for creating a surface grain boundary.
-
-    Args:
-        gap (float): The gap between the two phases.
-        xy_supercell_matrix (List[List[int]]): The supercell matrix to apply for both phases.
-    """
-
-    gap: float = 0.0
-    xy_supercell_matrix: List[List[int]] = [[1, 0], [0, 1]]
-
-    @property
-    def _json(self):
-        return {
-            "type": self.get_cls_name(),
-            "gap": self.gap,
-            "xy_supercell_matrix": self.xy_supercell_matrix,
-        }
-
-
-class SurfaceGrainBoundaryBuilderParameters(CommensurateLatticeTwistedInterfaceBuilderParameters):
-    """
-    Parameters for creating a grain boundary between two surface phases.
-
-    Args:
-        distance_tolerance (float): The distance tolerance to remove atoms that are too close, in angstroms.
-    """
-
-    distance_tolerance: float = 1.0
-
-
-class SurfaceGrainBoundaryBuilder(CommensurateLatticeTwistedInterfaceBuilder):
-    _ConfigurationType: type(SurfaceGrainBoundaryConfiguration) = SurfaceGrainBoundaryConfiguration  # type: ignore
-    _BuildParametersType = SurfaceGrainBoundaryBuilderParameters
-    _DefaultBuildParameters = SurfaceGrainBoundaryBuilderParameters()
-
-    def _post_process(self, items: List[Material], post_process_parameters=None) -> List[Material]:
-        grain_boundaries = []
-        for item in items:
-            matrix1 = np.dot(np.array(item.configuration.xy_supercell_matrix), item.matrix1)
-            matrix2 = np.dot(np.array(item.configuration.xy_supercell_matrix), item.matrix2)
-            phase_1_material_initial = create_supercell(item.configuration.film, matrix1.tolist())
-            phase_2_material_initial = create_supercell(item.configuration.film, matrix2.tolist())
-
-            interface = merge_two_materials_laterally(
-                phase_1_material_initial,
-                phase_2_material_initial,
-                gap=item.configuration.gap,
-                distance_tolerance=self.build_parameters.distance_tolerance,
-            )
-            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
+from .configuration import SurfaceGrainBoundaryConfiguration
+from .builders import SurfaceGrainBoundaryBuilder, SurfaceGrainBoundaryBuilderParameters

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

@@ -0,0 +1,53 @@
+from typing import List
+
+import numpy as np
+
+from mat3ra.made.material import Material
+
+
+from ..interface.builders import (
+    CommensurateLatticeTwistedInterfaceBuilder,
+    CommensurateLatticeTwistedInterfaceBuilderParameters,
+)
+from ..supercell import create_supercell
+from ..utils import merge_two_materials_laterally
+from .configuration import SurfaceGrainBoundaryConfiguration
+
+
+class SurfaceGrainBoundaryBuilderParameters(CommensurateLatticeTwistedInterfaceBuilderParameters):
+    """
+    Parameters for creating a grain boundary between two surface phases.
+
+    Args:
+        distance_tolerance (float): The distance tolerance to remove atoms that are too close, in angstroms.
+    """
+
+    distance_tolerance: float = 1.0
+
+
+class SurfaceGrainBoundaryBuilder(CommensurateLatticeTwistedInterfaceBuilder):
+    _ConfigurationType: type(SurfaceGrainBoundaryConfiguration) = SurfaceGrainBoundaryConfiguration  # type: ignore
+    _BuildParametersType = SurfaceGrainBoundaryBuilderParameters
+    _DefaultBuildParameters = SurfaceGrainBoundaryBuilderParameters()
+
+    def _post_process(self, items: List[Material], post_process_parameters=None) -> List[Material]:
+        grain_boundaries = []
+        for item in items:
+            matrix1 = np.dot(np.array(item.configuration.xy_supercell_matrix), item.matrix1)
+            matrix2 = np.dot(np.array(item.configuration.xy_supercell_matrix), item.matrix2)
+            phase_1_material_initial = create_supercell(item.configuration.film, matrix1.tolist())
+            phase_2_material_initial = create_supercell(item.configuration.film, matrix2.tolist())
+
+            interface = merge_two_materials_laterally(
+                phase_1_material_initial,
+                phase_2_material_initial,
+                gap=item.configuration.gap,
+                distance_tolerance=self.build_parameters.distance_tolerance,
+            )
+            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

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

@@ -0,0 +1,24 @@
+from typing import List
+
+from ..interface.configuration import TwistedInterfaceConfiguration
+
+
+class SurfaceGrainBoundaryConfiguration(TwistedInterfaceConfiguration):
+    """
+    Configuration for creating a surface grain boundary.
+
+    Args:
+        gap (float): The gap between the two phases.
+        xy_supercell_matrix (List[List[int]]): The supercell matrix to apply for both phases.
+    """
+
+    gap: float = 0.0
+    xy_supercell_matrix: List[List[int]] = [[1, 0], [0, 1]]
+
+    @property
+    def _json(self):
+        return {
+            "type": self.get_cls_name(),
+            "gap": self.gap,
+            "xy_supercell_matrix": self.xy_supercell_matrix,
+        }