update/SOF 7453

src/py/mat3ra/made/lattice.py

@@ -12,6 +12,16 @@
 DEFAULT_TYPE = "TRI"
 
 
+class LatticeVectors(BaseModel):
+    """
+    A class to represent the lattice vectors.
+    """
+
+    a: List[float] = [1.0, 0.0, 0.0]
+    b: List[float] = [0.0, 1.0, 0.0]
+    c: List[float] = [0.0, 0.0, 1.0]
+
+
 class Lattice(RoundNumericValuesMixin, BaseModel):
     a: float = 1.0
     b: float = a
@@ -23,7 +33,7 @@ class Lattice(RoundNumericValuesMixin, BaseModel):
     type: str = DEFAULT_TYPE
 
     @property
-    def vectors(self) -> List[List[float]]:
+    def vectors(self) -> LatticeVectors:
         a = self.a
         b = self.b
         c = self.c
@@ -44,12 +54,12 @@ def vectors(self) -> List[List[float]]:
         cos_gamma_star = math.cos(gamma_star)
         sin_gamma_star = math.sin(gamma_star)
 
-        # Return the lattice matrix using the derived trigonometric values
-        return [
-            [a * sin_beta, 0.0, a * cos_beta],
-            [-b * sin_alpha * cos_gamma_star, b * sin_alpha * sin_gamma_star, b * cos_alpha],
-            [0.0, 0.0, c],
-        ]
+        # Calculate the vectors
+        vector_a = [a * sin_beta, 0.0, a * cos_beta]
+        vector_b = [-b * sin_alpha * cos_gamma_star, b * sin_alpha * sin_gamma_star, b * cos_alpha]
+        vector_c = [0.0, 0.0, c]
+
+        return LatticeVectors(a=vector_a, b=vector_b, c=vector_c)
 
     @classmethod
     def from_vectors_array(
@@ -96,7 +106,9 @@ def clone(self, extra_context: Optional[Dict[str, Any]] = None) -> "Lattice":
 
     @property
     def vector_arrays(self) -> List[List[float]]:
-        return self.vectors
+        """Returns lattice vectors as a nested array"""
+        v = self.vectors
+        return [v.a, v.b, v.c]
 
     @property
     def cell(self) -> Cell:

src/py/mat3ra/made/material.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Optional, Union
 
 from mat3ra.code.constants import AtomicCoordinateUnits, Units
 from mat3ra.code.entity import HasDescriptionHasMetadataNamedDefaultableInMemoryEntity
@@ -112,3 +112,58 @@ def add_atom(self, element: str, coordinate: List[float], use_cartesian_coordina
         new_basis = self.basis.copy()
         new_basis.add_atom(element, coordinate, use_cartesian_coordinates)
         self.basis = new_basis
+
+    @classmethod
+    def create_empty(
+        cls,
+        a: float = 1.0,
+        b: Optional[float] = None,
+        c: Optional[float] = None,
+        alpha: float = 90.0,
+        beta: float = 90.0,
+        gamma: float = 90.0,
+        lattice_type: str = "CUB",
+        name: str = "New Material",
+    ) -> "Material":
+        """
+        Create an empty material with specified lattice parameters.
+
+        Args:
+            a (float): First lattice constant. Defaults to 1.0.
+            b (float, optional): Second lattice constant. Defaults to value of 'a'.
+            c (float, optional): Third lattice constant. Defaults to value of 'a'.
+            alpha (float): First lattice angle in degrees. Defaults to 90.0.
+            beta (float): Second lattice angle in degrees. Defaults to 90.0.
+            gamma (float): Third lattice angle in degrees. Defaults to 90.0.
+            lattice_type (str): Type of lattice. Defaults to "CUB".
+            name (str): Name of the material. Defaults to "New Material".
+
+        Returns:
+            Material: A new empty Material instance with specified lattice
+        """
+        b = b if b is not None else a
+        c = c if c is not None else a
+
+        basis_config = {
+            "elements": [],
+            "coordinates": [],
+            "units": AtomicCoordinateUnits.cartesian,
+        }
+
+        lattice_config = {
+            "type": lattice_type,
+            "a": a,
+            "b": b,
+            "c": c,
+            "alpha": alpha,
+            "beta": beta,
+            "gamma": gamma,
+            "units": {
+                "length": Units.angstrom,
+                "angle": Units.degree,
+            },
+        }
+
+        config = {"name": name, "basis": basis_config, "lattice": lattice_config}
+
+        return cls(config)

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

@@ -73,11 +73,11 @@ def _calculate_cartesian_dimensions(config: NanoribbonConfiguration, material: M
             nanoribbon_length, nanoribbon_width = nanoribbon_width, nanoribbon_length
             vacuum_width, vacuum_length = vacuum_length, vacuum_width
 
-        length_cartesian = nanoribbon_length * np.dot(np.array(material.lattice.vectors[0]), np.array([1, 0, 0]))
-        width_cartesian = nanoribbon_width * np.dot(np.array(material.lattice.vectors[1]), np.array([0, 1, 0]))
-        height_cartesian = np.dot(np.array(material.lattice.vectors[2]), np.array([0, 0, 1]))
-        vacuum_length_cartesian = vacuum_length * np.dot(np.array(material.lattice.vectors[0]), np.array([1, 0, 0]))
-        vacuum_width_cartesian = vacuum_width * np.dot(np.array(material.lattice.vectors[1]), np.array([0, 1, 0]))
+        length_cartesian = nanoribbon_length * np.dot(np.array(material.lattice.vectors.a), np.array([1, 0, 0]))
+        width_cartesian = nanoribbon_width * np.dot(np.array(material.lattice.vectors.b), np.array([0, 1, 0]))
+        height_cartesian = np.dot(np.array(material.lattice.vectors.c), np.array([0, 0, 1]))
+        vacuum_length_cartesian = vacuum_length * np.dot(np.array(material.lattice.vectors.a), np.array([1, 0, 0]))
+        vacuum_width_cartesian = vacuum_width * np.dot(np.array(material.lattice.vectors.b), np.array([0, 1, 0]))
 
         return length_cartesian, width_cartesian, height_cartesian, vacuum_length_cartesian, vacuum_width_cartesian
 

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

@@ -1,4 +1,5 @@
-from typing import Union, List
+from collections import Counter
+from typing import Union, List, Dict
 
 from mat3ra.made.material import Material
 from .configuration import PassivationConfiguration
@@ -36,3 +37,23 @@ def get_unique_coordination_numbers(
     material_with_crystal_sites = MaterialWithCrystalSites.from_material(configuration.slab)
     material_with_crystal_sites.analyze()
     return material_with_crystal_sites.get_unique_coordination_numbers(cutoff=cutoff)
+
+def get_coordination_numbers_distribution(
+    configuration: PassivationConfiguration,
+    cutoff: float = 3.0,
+) -> Dict[int, int]:
+    """
+    Get the unique coordination numbers for the provided passivation configuration and cutoff radius.
+
+    Args:
+        configuration (PassivationConfiguration): The configuration object.
+        cutoff (float): The cutoff radius for defining neighbors.
+    Returns:
+        set: The unique coordination numbers.
+    """
+    material_with_crystal_sites = MaterialWithCrystalSites.from_material(configuration.slab)
+    material_with_crystal_sites.analyze()
+    coordinatation_numbers = material_with_crystal_sites.get_coordination_numbers(cutoff=cutoff)
+    sorted_coordinatation_numbers = sorted(coordinatation_numbers.values)
+    distribution = dict(Counter(sorted_coordinatation_numbers))
+    return distribution

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

@@ -65,7 +65,7 @@ def create_perturbed_slab(self, configuration: PerturbationConfiguration) -> Mat
 
 class CellMatchingDistancePreservingSlabPerturbationBuilder(DistancePreservingSlabPerturbationBuilder):
     def _transform_lattice_vectors(self, configuration: PerturbationConfiguration) -> List[List[float]]:
-        cell_vectors = configuration.material.lattice.vectors
+        cell_vectors = configuration.material.lattice.vector_arrays
         return [configuration.perturbation_function_holder.transform_coordinates(coord) for coord in cell_vectors]
 
     def create_perturbed_slab(self, configuration: PerturbationConfiguration) -> Material: