@mat3ra/made 2024.11.1-0 → 2024.11.7-0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2024.11.1-0",
+    "version": "2024.11.7-0",
     "description": "MAterials DEsign library",
     "scripts": {
         "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js",

package/src/py/mat3ra/made/tools/build/defect/__init__.py

@@ -80,11 +80,19 @@ def create_slab_defect(
 
     Args:
         configuration: The configuration of the defect to be added.
-        builder: The builder to be used to create the defect.
+        builder: Optional builder to be used to create the defect.
+            If None, builder will be selected based on configuration.
 
     Returns:
         The material with the defect added.
     """
     if builder is None:
-        builder = AdatomSlabDefectBuilder(build_parameters=SlabDefectBuilderParameters())
+        if configuration.defect_type == PointDefectTypeEnum.ADATOM:
+            builder_key = f"adatom:{configuration.placement_method.lower()}"
+        else:
+            builder_key = configuration.defect_type.lower()
+
+        BuilderClass = DefectBuilderFactory.get_class_by_name(builder_key)
+        builder = BuilderClass(build_parameters=SlabDefectBuilderParameters())
+
     return builder.get_material(configuration)

package/src/py/mat3ra/made/tools/build/interface/builders.py

@@ -15,6 +15,7 @@ from ...modify import (
     rotate,
     translate_by_vector,
     add_vacuum_sides,
+    add_vacuum,
 )
 from ...analyze import get_chemical_formula
 from ...convert import to_ase, from_ase, to_pymatgen, PymatgenInterface, ASEAtoms
@@ -28,7 +29,7 @@ from ..mixins import (
     ConvertGeneratedItemsPymatgenStructureMixin,
 )
 
-from .enums import StrainModes
+from .enums import StrainModes, angle_to_supercell_matrix_values_for_hex
 from .configuration import (
     InterfaceConfiguration,
     NanoRibbonTwistedInterfaceConfiguration,
@@ -243,7 +244,7 @@ class NanoRibbonTwistedInterfaceBuilder(BaseBuilder):
     def _update_material_name(
         self, material: Material, configuration: NanoRibbonTwistedInterfaceConfiguration
     ) -> Material:
-        material.name = f"Twisted Nanoribbon Interface ({configuration.twist_angle:.2f}°)"
+        material.name = f"Twisted Nanoribbon Interface ({configuration.twist_angle:.2f} degrees)"
         return material
 
 
@@ -252,13 +253,16 @@ class CommensurateLatticeTwistedInterfaceBuilderParameters(BaseModel):
     Parameters for the commensurate lattice interface builder.
 
     Args:
-        max_repetition_int (int): The maximum search range for commensurate lattices.
+        max_supercell_matrix_int (Optional[int]): The maximum integer for the transformation matrices.
+            If not provided, it will be determined based on the target angle and the lattice vectors automatically.
+        limit_max_int (Optional[int]): The limit for the maximum integer for the transformation matrices when searching
         angle_tolerance (float): The tolerance for the angle between the commensurate lattices
             and the target angle, in degrees.
         return_first_match (bool): Whether to return the first match or all matches.
     """
 
-    max_repetition_int: int = 10
+    max_supercell_matrix_int: Optional[int] = None
+    limit_max_int: Optional[int] = 42
     angle_tolerance: float = 0.1
     return_first_match: bool = False
 
@@ -270,36 +274,65 @@ class CommensurateLatticeTwistedInterfaceBuilder(BaseBuilder):
     def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:
         film = configuration.film
         # substrate = configuration.substrate
-        max_search = self.build_parameters.max_repetition_int
         a = film.lattice.vector_arrays[0][:2]
         b = film.lattice.vector_arrays[1][:2]
-        commensurate_lattice_pairs = self.__generate_commensurate_lattices(
-            configuration, a, b, max_search, configuration.twist_angle
+        max_int = self.build_parameters.max_supercell_matrix_int or self.__get_initial_guess_for_max_int(
+            film, configuration.twist_angle
         )
+        commensurate_lattice_pairs: List[CommensurateLatticePair] = []
+        while not commensurate_lattice_pairs and max_int < self.build_parameters.limit_max_int:
+            print(f"Trying max_int = {max_int}")
+            commensurate_lattice_pairs = self.__generate_commensurate_lattices(
+                configuration, a, b, max_int, configuration.twist_angle
+            )
+            max_int += 1
+
         return commensurate_lattice_pairs
 
+    def __get_initial_guess_for_max_int(self, film, target_angle: float) -> int:
+        """
+        Determine the maximum integer for the transformation matrices based on the target angle.
+
+        Args:
+            a (List[float]): The a lattice vector.
+            b (List[float]): The b lattice vector.
+            target_angle (float): The target twist angle, in degrees.
+
+        Returns:
+            int: The maximum integer for the transformation matrices.
+        """
+        if film.lattice.type == "HEX":
+            # getting max int of the matrix that has angle closest to target angle
+            xy_supercell_matrix_for_closest_angle = min(
+                angle_to_supercell_matrix_values_for_hex, key=lambda x: abs(x["angle"] - target_angle)
+            )
+            # Get maximum absolute value from the supercell matrix values
+            return max(abs(x) for row in xy_supercell_matrix_for_closest_angle["xy_supercell"] for x in row)
+        return 1
+
     def __generate_commensurate_lattices(
         self,
         configuration: TwistedInterfaceConfiguration,
         a: List[float],
         b: List[float],
-        max_search: int = 10,
+        max_supercell_matrix_element_int: int,
         target_angle: float = 0.0,
     ) -> List[CommensurateLatticePair]:
         """
-        Generate all commensurate lattices for a given search range and filter by closeness to target angle.
+        Generate all commensurate lattices for a given target angle and filter by closeness to target angle.
 
         Args:
             configuration (TwistedInterfaceConfiguration): The configuration for the twisted interface.
             a (List[float]): The a lattice vector.
             b (List[float]): The b lattice vector.
-            max_search (int): The maximum search range.
-            target_angle (float): The target angle, in degrees.
+            max_supercell_matrix_element_int (int): The maximum integer for the transformation matrices.
+            target_angle (float): The target twist angle, in degrees.
 
         Returns:
             List[CommensurateLatticePair]: The list of commensurate lattice pairs
         """
-        matrices = create_2d_supercell_matrices(max_search)
+        # Generate the supercell matrices using the calculated max_supercell_matrix_element_int
+        matrices = create_2d_supercell_matrices(max_supercell_matrix_element_int)
         matrix_ab = np.array([a, b])
         matrix_ab_inverse = np.linalg.inv(matrix_ab)
 
@@ -342,8 +375,10 @@ class CommensurateLatticeTwistedInterfaceBuilder(BaseBuilder):
             new_film = translate_by_vector(
                 new_film, [0, 0, item.configuration.distance_z], use_cartesian_coordinates=True
             )
-            interface = merge_materials([new_substrate, new_film])
+            interface = merge_materials([new_substrate, new_film], merge_dangerously=True)
             interface.metadata["actual_twist_angle"] = item.angle
+            if item.configuration.vacuum != 0:
+                interface = add_vacuum(interface, item.configuration.vacuum)
             interfaces.append(interface)
         return interfaces
 
@@ -354,3 +389,9 @@ class CommensurateLatticeTwistedInterfaceBuilder(BaseBuilder):
                 "actual_twist_angle"
             ]
         return updated_material
+
+    def _update_material_name(
+        self, material: Material, configuration: NanoRibbonTwistedInterfaceConfiguration
+    ) -> Material:
+        material.name = f"Twisted Bilayer Interface ({material.metadata['actual_twist_angle']:.2f} degrees)"
+        return material

package/src/py/mat3ra/made/tools/build/interface/configuration.py

@@ -40,6 +40,7 @@ class TwistedInterfaceConfiguration(BaseConfiguration):
     substrate: Optional[Material] = None
     twist_angle: float = 0.0
     distance_z: float = 3.0
+    vacuum: float = 0.0
 
     @property
     def _json(self):

package/src/py/mat3ra/made/tools/build/interface/enums.py

@@ -1,4 +1,5 @@
 from enum import Enum
+from typing import TypedDict, List
 
 
 class StrainModes(str, Enum):
@@ -10,3 +11,56 @@ class StrainModes(str, Enum):
 class SupercellTypes(str, Enum):
     hexagonal = "hexagonal"
     orthogonal = "orthogonal"
+
+
+class SupercellMatrix(TypedDict):
+    angle: float
+    xy_supercell: List[List[int]]
+
+
+# Tabulation from https://github.com/qtm-iisc/Twister/blob/474156a2a59f2b9d59350b32de56864a9496f848/examples/Homobilayer_hex/hex.table
+# Maps twist angle to supercell matrix values for homo-material hexagonal supercells bilayer
+angle_to_supercell_matrix_values_for_hex: List[SupercellMatrix] = [
+    {"angle": 60.0, "xy_supercell": [[0, 1], [-1, 1]]},
+    {"angle": 21.7867892983, "xy_supercell": [[1, 2], [-2, 3]]},
+    {"angle": 13.1735511073, "xy_supercell": [[2, 3], [-3, 5]]},
+    {"angle": 9.4300079079, "xy_supercell": [[3, 4], [-4, 7]]},
+    {"angle": 7.34099301663, "xy_supercell": [[4, 5], [-5, 9]]},
+    {"angle": 6.00898319777, "xy_supercell": [[5, 6], [-6, 11]]},
+    {"angle": 5.08584780812, "xy_supercell": [[6, 7], [-7, 13]]},
+    {"angle": 4.40845500794, "xy_supercell": [[7, 8], [-8, 15]]},
+    {"angle": 3.89023816901, "xy_supercell": [[8, 9], [-9, 17]]},
+    {"angle": 3.48100608947, "xy_supercell": [[9, 10], [-10, 19]]},
+    {"angle": 3.14965742639, "xy_supercell": [[10, 11], [-11, 21]]},
+    {"angle": 2.87589463363, "xy_supercell": [[11, 12], [-12, 23]]},
+    {"angle": 2.64590838119, "xy_supercell": [[12, 13], [-13, 25]]},
+    {"angle": 2.44997727662, "xy_supercell": [[13, 14], [-14, 27]]},
+    {"angle": 2.28105960973, "xy_supercell": [[14, 15], [-15, 29]]},
+    {"angle": 2.1339296666, "xy_supercell": [[15, 16], [-16, 31]]},
+    {"angle": 2.00462783069, "xy_supercell": [[16, 17], [-17, 33]]},
+    {"angle": 1.89009907347, "xy_supercell": [[17, 18], [-18, 35]]},
+    {"angle": 1.78794861038, "xy_supercell": [[18, 19], [-19, 37]]},
+    {"angle": 1.69627269352, "xy_supercell": [[19, 20], [-20, 39]]},
+    {"angle": 1.61353890116, "xy_supercell": [[20, 21], [-21, 41]]},
+    {"angle": 1.53849981837, "xy_supercell": [[21, 22], [-22, 43]]},
+    {"angle": 1.47012972578, "xy_supercell": [[22, 23], [-23, 45]]},
+    {"angle": 1.40757744635, "xy_supercell": [[23, 24], [-24, 47]]},
+    {"angle": 1.35013073557, "xy_supercell": [[24, 25], [-25, 49]]},
+    {"angle": 1.29718904759, "xy_supercell": [[25, 26], [-26, 51]]},
+    {"angle": 1.24824246553, "xy_supercell": [[26, 27], [-27, 53]]},
+    {"angle": 1.20285522748, "xy_supercell": [[27, 28], [-28, 55]]},
+    {"angle": 1.16065271985, "xy_supercell": [[28, 29], [-29, 57]]},
+    {"angle": 1.12131111538, "xy_supercell": [[29, 30], [-30, 59]]},
+    {"angle": 1.08454904916, "xy_supercell": [[30, 31], [-31, 61]]},
+    {"angle": 1.05012087979, "xy_supercell": [[31, 32], [-32, 63]]},
+    {"angle": 1.01781119445, "xy_supercell": [[32, 33], [-33, 65]]},
+    {"angle": 0.987430297814, "xy_supercell": [[33, 34], [-34, 67]]},
+    {"angle": 0.958810485525, "xy_supercell": [[34, 35], [-35, 69]]},
+    {"angle": 0.931802947264, "xy_supercell": [[35, 36], [-36, 71]]},
+    {"angle": 0.906275178895, "xy_supercell": [[36, 37], [-37, 73]]},
+    {"angle": 0.882108808579, "xy_supercell": [[37, 38], [-38, 75]]},
+    {"angle": 0.859197761631, "xy_supercell": [[38, 39], [-39, 77]]},
+    {"angle": 0.8374467041, "xy_supercell": [[39, 40], [-40, 79]]},
+    {"angle": 0.816769716893, "xy_supercell": [[40, 41], [-41, 81]]},
+    {"angle": 0.0, "xy_supercell": [[1, 0], [0, 1]]},
+]