update: add gap between phases

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

@@ -7,8 +7,7 @@
 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 filter_by_box
-
+from mat3ra.made.tools.modify import filter_by_box, add_vacuum_sides, translate_by_vector
 
 from mat3ra.made.tools.build.interface.configuration import TwistedInterfaceConfiguration
 
@@ -44,6 +43,26 @@ def _post_process(self, items: List[Material], post_process_parameters=None) ->
             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])
 
+            new_lattice_vectors_1 = phase_1_material.lattice.vector_arrays
+            new_lattice_vectors_1[0][0] += item.configuration.gap
+
+            new_lattice_vectors_2 = phase_2_material.lattice.vector_arrays
+            new_lattice_vectors_2[0][0] += item.configuration.gap
+            phase_1_material.set_new_lattice_vectors(
+                lattice_vector1=new_lattice_vectors_1[0],
+                lattice_vector2=new_lattice_vectors_1[1],
+                lattice_vector3=new_lattice_vectors_1[2],
+            )
+            phase_2_material.set_new_lattice_vectors(
+                lattice_vector1=new_lattice_vectors_2[0],
+                lattice_vector2=new_lattice_vectors_2[1],
+                lattice_vector3=new_lattice_vectors_2[2],
+            )
+
+            phase_2_material = translate_by_vector(
+                phase_2_material, [item.configuration.gap / 2, 0, 0], use_cartesian_coordinates=True
+            )
+
             interface = merge_materials([phase_1_material, phase_2_material])
             grain_boundaries.append(interface)