@mat3ra/made 2024.9.28-0 → 2024.10.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2024.9.28-0",
+    "version": "2024.10.1-0",
     "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/grain_boundary/__init__.py

@@ -1,14 +1,17 @@
-from typing import Optional
+from typing import Optional, Union
 
 from mat3ra.made.material import Material
 
-from .builders import SlabGrainBoundaryBuilder
-from .configuration import SlabGrainBoundaryConfiguration
+from .builders import SlabGrainBoundaryBuilder, SurfaceGrainBoundaryBuilder, SurfaceGrainBoundaryBuilderParameters
+from .configuration import (
+    SlabGrainBoundaryConfiguration,
+    SurfaceGrainBoundaryConfiguration,
+)
 
 
 def create_grain_boundary(
-    configuration: SlabGrainBoundaryConfiguration,
-    builder: Optional[SlabGrainBoundaryBuilder] = None,
+    configuration: Union[SlabGrainBoundaryConfiguration, SurfaceGrainBoundaryConfiguration],
+    builder: Union[SlabGrainBoundaryBuilder, SurfaceGrainBoundaryBuilder, None] = None,
 ) -> Material:
     """
     Create a grain boundary according to provided configuration with selected builder.

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

@@ -3,13 +3,19 @@ from typing import List
 import numpy as np
 from mat3ra.made.material import Material
 
-from ..slab import SlabConfiguration, get_terminations, create_slab
+from ...third_party import PymatgenInterface
 from ...analyze import get_chemical_formula
+from ..slab import SlabConfiguration, get_terminations, create_slab
 from ..interface import ZSLStrainMatchingInterfaceBuilderParameters, InterfaceConfiguration
-from ..interface.builders import ZSLStrainMatchingInterfaceBuilder
+
+from ..interface.builders import (
+    ZSLStrainMatchingInterfaceBuilder,
+    CommensurateLatticeTwistedInterfaceBuilder,
+    CommensurateLatticeTwistedInterfaceBuilderParameters,
+)
 from ..supercell import create_supercell
-from .configuration import SlabGrainBoundaryConfiguration
-from ...third_party import PymatgenInterface
+from ..utils import stack_two_materials_xy
+from .configuration import SurfaceGrainBoundaryConfiguration, SlabGrainBoundaryConfiguration
 
 
 class SlabGrainBoundaryBuilderParameters(ZSLStrainMatchingInterfaceBuilderParameters):
@@ -27,6 +33,7 @@ class SlabGrainBoundaryBuilder(ZSLStrainMatchingInterfaceBuilder):
     """
 
     _BuildParametersType: type(SlabGrainBoundaryBuilderParameters) = SlabGrainBoundaryBuilderParameters  # type: ignore
+    _DefaultBuildParameters = SlabGrainBoundaryBuilderParameters()
     _ConfigurationType: type(SlabGrainBoundaryConfiguration) = SlabGrainBoundaryConfiguration  # type: ignore
     _GeneratedItemType: PymatgenInterface = PymatgenInterface  # type: ignore
     selector_parameters: type(  # type: ignore
@@ -78,3 +85,46 @@ class SlabGrainBoundaryBuilder(ZSLStrainMatchingInterfaceBuilder):
         )
         material.name = new_name
         return material
+
+
+class SurfaceGrainBoundaryBuilderParameters(CommensurateLatticeTwistedInterfaceBuilderParameters):
+    """
+    Parameters for creating a grain boundary between two surface phases.
+
+    Args:
+        edge_inclusion_tolerance (float): The tolerance to include atoms on the edge of each phase, in angstroms.
+        distance_tolerance (float): The distance tolerance to remove atoms that are too close, in angstroms.
+    """
+
+    edge_inclusion_tolerance: float = 1.0
+    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 = stack_two_materials_xy(
+                phase_1_material_initial,
+                phase_2_material_initial,
+                gap=item.configuration.gap,
+                edge_inclusion_tolerance=self.build_parameters.edge_inclusion_tolerance,
+                distance_tolerance=self.build_parameters.distance_tolerance,
+            )
+            grain_boundaries.append(interface)
+
+        return grain_boundaries
+
+    def _update_material_name(self, material: Material, configuration: SurfaceGrainBoundaryConfiguration) -> Material:
+        new_name = f"{configuration.film.name}, Grain Boundary ({configuration.twist_angle:.2f}°)"
+        material.name = new_name
+        return material

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

@@ -1,8 +1,9 @@
-from typing import Optional
+from typing import Optional, List
 
 from .. import BaseConfiguration
 from ..slab.configuration import SlabConfiguration
 from ..slab.termination import Termination
+from ..interface.configuration import TwistedInterfaceConfiguration
 
 
 class SlabGrainBoundaryConfiguration(BaseConfiguration):
@@ -38,3 +39,24 @@ class SlabGrainBoundaryConfiguration(BaseConfiguration):
             "gap": self.gap,
             "slab_configuration": self.slab_configuration.to_json(),
         }
+
+
+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,
+        }

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

@@ -247,7 +247,7 @@ class NanoRibbonTwistedInterfaceBuilder(BaseBuilder):
         return material
 
 
-class CommensurateLatticeInterfaceBuilderParameters(BaseModel):
+class CommensurateLatticeTwistedInterfaceBuilderParameters(BaseModel):
     """
     Parameters for the commensurate lattice interface builder.
 
@@ -263,7 +263,7 @@ class CommensurateLatticeInterfaceBuilderParameters(BaseModel):
     return_first_match: bool = False
 
 
-class CommensurateLatticeInterfaceBuilder(BaseBuilder):
+class CommensurateLatticeTwistedInterfaceBuilder(BaseBuilder):
     _GeneratedItemType: type(CommensurateLatticePair) = CommensurateLatticePair  # type: ignore
     _ConfigurationType: type(TwistedInterfaceConfiguration) = TwistedInterfaceConfiguration  # type: ignore
 

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

@@ -1,3 +1,5 @@
+from typing import Optional
+
 from mat3ra.code.entity import InMemoryEntity
 from pydantic import BaseModel
 
@@ -35,7 +37,7 @@ class InterfaceConfiguration(BaseModel, InMemoryEntity):
 
 class TwistedInterfaceConfiguration(BaseConfiguration):
     film: Material
-    substrate: Material
+    substrate: Optional[Material] = None
     twist_angle: float = 0.0
     distance_z: float = 3.0
 
@@ -44,7 +46,7 @@ class TwistedInterfaceConfiguration(BaseConfiguration):
         return {
             "type": self.get_cls_name(),
             "film": self.film.to_json(),
-            "substrate": self.substrate.to_json(),
+            "substrate": self.substrate.to_json() if self.substrate else None,
             "twist_angle": self.twist_angle,
             "distance_z": self.distance_z,
         }

package/src/py/mat3ra/made/tools/build/utils.py

@@ -3,6 +3,9 @@ from scipy.spatial import cKDTree
 from typing import List, Optional
 from mat3ra.made.basis import Basis
 from mat3ra.made.material import Material
+
+from .supercell import create_supercell
+from ..modify import filter_by_box, translate_by_vector
 from ...utils import ArrayWithIds
 
 
@@ -78,6 +81,20 @@ def merge_materials(
     distance_tolerance: float = 0.01,
     merge_dangerously=False,
 ) -> Material:
+    """
+    Merge multiple materials into a single material.
+
+    If some of the atoms are considered too close within a tolerance, only the last atom is kept.
+
+    Args:
+        materials (List[Material]): List of materials to merge.
+        material_name (Optional[str]): Name of the merged material.
+        distance_tolerance (float): The tolerance to replace atoms that are considered too close with respect
+            to the coordinates in the last material in the list, in angstroms.
+        merge_dangerously (bool): If True, the lattices are merged "as is" with no sanity checks.
+    Returns:
+        Material: The merged material.
+    """
     merged_material = materials[0]
     for material in materials[1:]:
         merged_material = merge_two_materials(
@@ -85,3 +102,77 @@ def merge_materials(
         )
 
     return merged_material
+
+
+def double_and_filter_material(material: Material, start: List[float], end: List[float]) -> Material:
+    """
+    Double the material and filter it by a box defined by the start and end coordinates.
+    Args:
+        material (Material): The material to double and filter.
+        start (List[float]): The start coordinates of the box.
+        end (List[float]): The end coordinates of the box.
+    Returns:
+        Material: The filtered material.
+    """
+    material_doubled = create_supercell(material, scaling_factor=[2, 1, 1])
+    return filter_by_box(material_doubled, start, end)
+
+
+def expand_lattice_vectors(material: Material, gap: float, direction: int = 0) -> Material:
+    """
+    Expand the lattice vectors of the material in the specified direction by the given gap.
+
+    Args:
+        material (Material): The material whose lattice vectors are to be expanded.
+        gap (float): The gap by which to expand the lattice vector.
+        direction (int): The index of the lattice vector to expand (0, 1, or 2).
+    """
+    new_lattice_vectors = material.lattice.vector_arrays
+    new_lattice_vectors[direction][direction] += gap
+    material.set_new_lattice_vectors(
+        lattice_vector1=new_lattice_vectors[0],
+        lattice_vector2=new_lattice_vectors[1],
+        lattice_vector3=new_lattice_vectors[2],
+    )
+    return material
+
+
+def stack_two_materials_xy(
+    phase_1_material: Material,
+    phase_2_material: Material,
+    gap: float,
+    edge_inclusion_tolerance: Optional[float] = 1.0,
+    distance_tolerance: float = 1.0,
+) -> Material:
+    """
+    Stack two materials laterally with translation along x-axis with a gap between them.
+
+    Works correctly only for materials with the same lattice vectors (commensurate lattices).
+     Args:
+        phase_1_material (Material): The first material.
+        phase_2_material (Material): The second material.
+        gap (float): The gap between the two materials, in angstroms.
+        edge_inclusion_tolerance (float): The tolerance to include atoms on the edge of the phase, in angstroms.
+        distance_tolerance (float): The distance tolerance to remove atoms that are too close, in angstroms.
+
+    Returns:
+        Material: The merged material.
+    """
+    edge_inclusion_tolerance_crystal = abs(
+        phase_1_material.basis.cell.convert_point_to_crystal([edge_inclusion_tolerance, 0, 0])[0]
+    )
+
+    phase_1_material = double_and_filter_material(
+        phase_1_material, [0 - edge_inclusion_tolerance_crystal, 0, 0], [0.5 + edge_inclusion_tolerance_crystal, 1, 1]
+    )
+
+    phase_2_material = double_and_filter_material(
+        phase_2_material, [0.5 - edge_inclusion_tolerance_crystal, 0, 0], [1 + edge_inclusion_tolerance_crystal, 1, 1]
+    )
+
+    phase_1_material = expand_lattice_vectors(phase_1_material, gap)
+    phase_2_material = expand_lattice_vectors(phase_2_material, gap)
+
+    phase_2_material = translate_by_vector(phase_2_material, [gap / 2, 0, 0], use_cartesian_coordinates=True)
+    interface = merge_materials([phase_1_material, phase_2_material], distance_tolerance=distance_tolerance)
+    return interface

package/tests/py/unit/test_tools_build_grain_boundary.py

@@ -2,12 +2,17 @@ from mat3ra.made.material import Material
 from mat3ra.made.tools.build.grain_boundary import (
     SlabGrainBoundaryBuilder,
     SlabGrainBoundaryConfiguration,
+    SurfaceGrainBoundaryBuilder,
+    SurfaceGrainBoundaryBuilderParameters,
+    SurfaceGrainBoundaryConfiguration,
     create_grain_boundary,
 )
-from mat3ra.made.tools.build.interface import ZSLStrainMatchingInterfaceBuilderParameters
+from mat3ra.made.tools.build.grain_boundary.builders import SlabGrainBoundaryBuilderParameters
 from mat3ra.made.tools.build.slab import SlabConfiguration, get_terminations
 from mat3ra.utils import assertion as assertion_utils
 
+from .fixtures import GRAPHENE
+
 
 def test_slab_grain_boundary_builder():
     material = Material(Material.default_config)
@@ -44,7 +49,7 @@ def test_slab_grain_boundary_builder():
         slab_configuration=slab_config,
     )
 
-    builder_params = ZSLStrainMatchingInterfaceBuilderParameters(max_area=50)
+    builder_params = SlabGrainBoundaryBuilderParameters()
     builder = SlabGrainBoundaryBuilder(build_parameters=builder_params)
     gb = create_grain_boundary(config, builder)
     expected_lattice_vectors = [
@@ -57,3 +62,30 @@ def test_slab_grain_boundary_builder():
     assert len(gb.basis.elements.values) == 32
     assertion_utils.assert_deep_almost_equal(expected_coordinate_15, gb.basis.coordinates.values[15])
     assertion_utils.assert_deep_almost_equal(expected_lattice_vectors, gb.lattice.vector_arrays)
+
+
+def test_create_surface_grain_boundary():
+    config = SurfaceGrainBoundaryConfiguration(
+        film=Material(GRAPHENE),
+        twist_angle=13.0,
+        gap=2.0,
+    )
+
+    builder_params = SurfaceGrainBoundaryBuilderParameters(
+        max_repetition_int=5,
+        angle_tolerance=0.5,
+        return_first_match=True,
+        distance_tolerance=1.0,
+    )
+    builder = SurfaceGrainBoundaryBuilder(build_parameters=builder_params)
+
+    gb = builder.get_materials(config)
+
+    expected_cell_vectors = [
+        [23.509344266, 0.0, 0.0],
+        [5.377336066500001, 9.313819276550575, 0.0],
+        [0.0, 0.0, 20.0],
+    ]
+
+    assert len(gb) == 1
+    assertion_utils.assert_deep_almost_equal(expected_cell_vectors, gb[0].basis.cell.vectors_as_array)

package/tests/py/unit/test_tools_build_interface.py

@@ -9,8 +9,8 @@ from mat3ra.made.tools.build.interface import (
     create_interfaces,
 )
 from mat3ra.made.tools.build.interface.builders import (
-    CommensurateLatticeInterfaceBuilder,
-    CommensurateLatticeInterfaceBuilderParameters,
+    CommensurateLatticeTwistedInterfaceBuilder,
+    CommensurateLatticeTwistedInterfaceBuilderParameters,
     NanoRibbonTwistedInterfaceBuilder,
     NanoRibbonTwistedInterfaceConfiguration,
     TwistedInterfaceConfiguration,
@@ -72,10 +72,10 @@ def test_create_commensurate_supercell_twisted_interface():
     film = Material(GRAPHENE)
     substrate = Material(GRAPHENE)
     config = TwistedInterfaceConfiguration(film=film, substrate=substrate, twist_angle=13, distance_z=3.0)
-    params = CommensurateLatticeInterfaceBuilderParameters(
+    params = CommensurateLatticeTwistedInterfaceBuilderParameters(
         max_repetition_int=5, angle_tolerance=0.5, return_first_match=True
     )
-    builder = CommensurateLatticeInterfaceBuilder(build_parameters=params)
+    builder = CommensurateLatticeTwistedInterfaceBuilder(build_parameters=params)
     interfaces = builder.get_materials(config, post_process_parameters=config)
     assert len(interfaces) == 1
     interface = interfaces[0]