update: actually pass parameters of passivation

Exabyte-io · Dec 11, 2024 · cde2528 · cde2528
1 parent 8cbf95e
commit cde2528
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/src/py/mat3ra/made/tools/analyze/material.py b/src/py/mat3ra/made/tools/analyze/material.py
@@ -184,7 +184,10 @@ def get_unique_coordination_numbers(self, cutoff: float) -> List[int]:
 
     @decorator_handle_periodic_boundary_conditions(cutoff=0.25)
     def find_missing_bonds_for_all_sites(
-        self, bond_templates_list: List[BondDirectionsTemplatesForElement]
+        self,
+        bond_templates_list: List[BondDirectionsTemplatesForElement],
+        max_bonds_to_add: int = 1,
+        angle_tolerance: float = 0.1,
     ) -> List[BondDirections]:
         """
         Find missing bonds for all sites in the material.
@@ -209,8 +212,8 @@ def find_missing_bonds_for_all_sites(
                 continue
             missing_bonds_for_site = existing_bond_directions.find_missing_directions(
                 bond_templates=bond_templates,
-                angle_tolerance=0.1,
-                max_bonds_to_add=1,
+                angle_tolerance=angle_tolerance,
+                max_bonds_to_add=max_bonds_to_add,
             )
             missing_bonds.append(BondDirections(missing_bonds_for_site))
 

diff --git a/src/py/mat3ra/made/tools/build/passivation/builders.py b/src/py/mat3ra/made/tools/build/passivation/builders.py
@@ -173,7 +173,11 @@ def create_passivated_material(self, configuration: PassivationConfiguration) ->
         )
         # TODO: bonds_templates will be passed from the configuration in the "controlled" version of this class
         bonds_templates = material_with_crystal_sites.find_unique_bond_directions()
-        reconstructed_bonds = material_with_crystal_sites.find_missing_bonds_for_all_sites(bonds_templates)
+        reconstructed_bonds = material_with_crystal_sites.find_missing_bonds_for_all_sites(
+            bond_templates_list=bonds_templates,
+            max_bonds_to_add=self.build_parameters.bonds_to_passivate,
+            angle_tolerance=self.build_parameters.symmetry_tolerance,
+        )
         passivant_coordinates_values = self._get_passivant_coordinates(
             material,
             configuration,