Merge pull request #165 from Exabyte-io/update/SOF-7461

Update/SOF-7461 Update: various cleanups

src/py/mat3ra/made/tools/analyze.py

@@ -7,7 +7,7 @@
 from .convert import decorator_convert_material_args_kwargs_to_atoms, to_pymatgen
 from .enums import SurfaceTypes
 from .third_party import ASEAtoms, PymatgenIStructure, PymatgenVoronoiNN
-from .utils import decorator_handle_periodic_boundary_conditions
+from .utils import decorator_convert_position_to_coordinate, decorator_handle_periodic_boundary_conditions
 
 
 @decorator_convert_material_args_kwargs_to_atoms
@@ -471,6 +471,7 @@ def get_undercoordinated_atom_indices(
     return undercoordinated_atoms_indices
 
 
+@decorator_convert_position_to_coordinate
 def get_local_extremum_atom_index(
     material: Material,
     coordinate: List[float],

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

@@ -15,11 +15,11 @@
 
 from ...modify import (
     add_vacuum,
-    filter_material_by_ids,
+    filter_by_ids,
     filter_by_box,
     filter_by_condition_on_coordinates,
     translate_to_z_level,
-    rotate_material,
+    rotate,
 )
 from ...build import BaseBuilder
 from ...convert import to_pymatgen
@@ -28,6 +28,7 @@
     get_atomic_coordinates_extremum,
     get_closest_site_id_from_coordinate,
     get_closest_site_id_from_coordinate_and_element,
+    get_local_extremum_atom_index,
 )
 from ....utils import get_center_of_coordinates
 from ...utils import transform_coordinate_to_supercell, coordinate as CoordinateCondition
@@ -174,7 +175,10 @@ def create_adatom(
     def _calculate_coordinate_from_position_and_distance(
         self, material: Material, position_on_surface: List[float], distance_z: float
     ) -> List[float]:
-        max_z = get_atomic_coordinates_extremum(material, use_cartesian_coordinates=False)
+        max_z_id = get_local_extremum_atom_index(
+            material, position_on_surface, "max", vicinity=3.0, use_cartesian_coordinates=False
+        )
+        max_z = material.basis.coordinates.get_element_value_by_index(max_z_id)[2]
         distance_in_crystal_units = distance_z / material.lattice.c
         return [position_on_surface[0], position_on_surface[1], max_z + distance_in_crystal_units]
 
@@ -290,7 +294,7 @@ def create_isolated_adatom(
             closest_site_id = get_closest_site_id_from_coordinate_and_element(
                 material, approximate_adatom_coordinate_cartesian, chemical_element
             )
-        only_adatom_material = filter_material_by_ids(material, [closest_site_id])
+        only_adatom_material = filter_by_ids(material, [closest_site_id])
         return only_adatom_material
 
     def create_adatom(
@@ -612,7 +616,7 @@ def create_terrace(
 
         if rotate_to_match_pbc:
             adjusted_material = self._increase_lattice_size(result_material, delta_length, normalized_direction_vector)
-            result_material = rotate_material(material=adjusted_material, axis=normalized_rotation_axis, angle=angle)
+            result_material = rotate(material=adjusted_material, axis=normalized_rotation_axis, angle=angle)
         return result_material
 
     def _generate(self, configuration: _ConfigurationType) -> List[_GeneratedItemType]:

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

@@ -4,7 +4,7 @@
 
 from mat3ra.made.material import Material
 from ...calculate.calculators import InterfaceMaterialCalculator
-from ...modify import displace_interface_part
+from ...modify import interface_displace_part
 from ...optimize import evaluate_calculator_on_xy_grid
 from .builders import (
     SimpleInterfaceBuilder,
@@ -64,7 +64,7 @@ def get_optimal_film_displacement(
     xy_matrix, results_matrix = evaluate_calculator_on_xy_grid(
         material=material,
         calculator_function=calculator.get_energy,
-        modifier=displace_interface_part,
+        modifier=interface_displace_part,
         modifier_parameters={},
         grid_size_xy=grid_size_xy,
         grid_offset_position=grid_offset_position,

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

@@ -12,7 +12,7 @@
 from ....utils import create_2d_supercell_matrices, get_angle_from_rotation_matrix_2d
 from ...modify import (
     translate_to_z_level,
-    rotate_material,
+    rotate,
     translate_by_vector,
     add_vacuum_sides,
 )
@@ -229,7 +229,7 @@ def _generate(self, configuration: _ConfigurationType) -> List[Material]:
             length=configuration.ribbon_length,
         )
         top_ribbon = create_nanoribbon(top_ribbon_configuration)
-        top_ribbon = rotate_material(top_ribbon, [0, 0, 1], configuration.twist_angle, wrap=False)
+        top_ribbon = rotate(top_ribbon, [0, 0, 1], configuration.twist_angle, wrap=False)
 
         translation_vector = [0, 0, configuration.distance_z]
         top_ribbon = translate_by_vector(top_ribbon, translation_vector, use_cartesian_coordinates=True)

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

@@ -1,4 +1,4 @@
-from typing import List
+from typing import List, Optional
 
 from mat3ra.made.material import Material
 from .builders import SlabBuilder, SlabSelectorParameters
@@ -10,6 +10,7 @@ def get_terminations(configuration: SlabConfiguration) -> List[Termination]:
     return SlabBuilder().get_terminations(configuration)
 
 
-def create_slab(configuration: SlabConfiguration, termination: Termination) -> Material:
+def create_slab(configuration: SlabConfiguration, termination: Optional[Termination] = None) -> Material:
     builder = SlabBuilder()
+    termination = termination or builder.get_terminations(configuration)[0]
     return builder.get_material(configuration, selector_parameters=SlabSelectorParameters(termination=termination))

src/py/mat3ra/made/tools/calculate/calculators.py

@@ -7,7 +7,7 @@
 from ..analyze import get_surface_atom_indices
 from ..convert.utils import InterfacePartsEnum
 from ..enums import SurfaceTypes
-from ..modify import get_interface_part
+from ..modify import interface_get_part
 from .interaction_functions import sum_of_inverse_distances_squared
 
 
@@ -101,8 +101,8 @@ def get_energy(
         Returns:
             float: The calculated interaction energy between the film and substrate.
         """
-        film_material = get_interface_part(material, part=InterfacePartsEnum.FILM)
-        substrate_material = get_interface_part(material, part=InterfacePartsEnum.SUBSTRATE)
+        film_material = interface_get_part(material, part=InterfacePartsEnum.FILM)
+        substrate_material = interface_get_part(material, part=InterfacePartsEnum.SUBSTRATE)
 
         film_surface_atom_indices = get_surface_atom_indices(
             film_material, SurfaceTypes.BOTTOM, shadowing_radius=shadowing_radius

src/py/mat3ra/made/tools/modify.py

@@ -128,7 +128,7 @@ def wrap_to_unit_cell(material: Material) -> Material:
     return Material(from_ase(atoms))
 
 
-def filter_material_by_ids(material: Material, ids: List[int], invert: bool = False) -> Material:
+def filter_by_ids(material: Material, ids: List[int], invert: bool = False) -> Material:
     """
     Filter out only atoms corresponding to the ids.
 
@@ -174,7 +174,7 @@ def filter_by_condition_on_coordinates(
         use_cartesian_coordinates=use_cartesian_coordinates,
     )
 
-    new_material = filter_material_by_ids(new_material, ids, invert=invert_selection)
+    new_material = filter_by_ids(new_material, ids, invert=invert_selection)
     return new_material
 
 
@@ -234,7 +234,7 @@ def filter_by_sphere(
         coordinate=center_coordinate,
         radius=radius,
     )
-    return filter_material_by_ids(material, ids, invert=invert)
+    return filter_by_ids(material, ids, invert=invert)
 
 
 def filter_by_circle_projection(
@@ -482,7 +482,7 @@ def remove_vacuum(material: Material, from_top=True, from_bottom=True, fixed_pad
     return new_material
 
 
-def rotate_material(material: Material, axis: List[int], angle: float, wrap: bool = True) -> Material:
+def rotate(material: Material, axis: List[int], angle: float, wrap: bool = True, rotate_cell=False) -> Material:
     """
     Rotate the material around a given axis by a specified angle.
 
@@ -491,6 +491,7 @@ def rotate_material(material: Material, axis: List[int], angle: float, wrap: boo
         axis (List[int]): The axis to rotate around, expressed as [x, y, z].
         angle (float): The angle of rotation in degrees.
         wrap (bool): Whether to wrap the material to the unit cell.
+        rotate_cell (bool): Whether to rotate the cell.
     Returns:
         Atoms: The rotated material.
     """
@@ -499,14 +500,14 @@ def rotate_material(material: Material, axis: List[int], angle: float, wrap: boo
         crystal_basis.to_crystal()
         material.basis = crystal_basis
     atoms = to_ase(material)
-    atoms.rotate(v=axis, a=angle, center="COU")
+    atoms.rotate(v=axis, a=angle, center="COU", rotate_cell=rotate_cell)
     if wrap:
         atoms.wrap()
 
     return Material(from_ase(atoms))
 
 
-def displace_interface_part(
+def interface_displace_part(
     interface: Material,
     displacement: List[float],
     label: InterfacePartsEnum = InterfacePartsEnum.FILM,
@@ -542,7 +543,7 @@ def displace_interface_part(
     return new_material
 
 
-def get_interface_part(
+def interface_get_part(
     interface: Material,
     part: InterfacePartsEnum = InterfacePartsEnum.FILM,
 ) -> Material:

src/py/mat3ra/made/tools/utils/__init__.py

@@ -1,5 +1,5 @@
 from functools import wraps
-from typing import Callable, List, Optional, Tuple
+from typing import Any, Callable, List, Optional, Tuple
 
 import numpy as np
 from mat3ra.made.material import Material
@@ -42,6 +42,35 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
+def decorator_convert_position_to_coordinate(func: Callable) -> Callable:
+    """
+    A decorator that converts a 2D position [x, y] to a 3D coordinate [x, y, 0.0].
+    """
+
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        if "coordinate" in kwargs:
+            coordinate = kwargs["coordinate"]
+        else:
+            # Find the position of the 'coordinate' argument and get its value
+            coordinate_index = func.__code__.co_varnames.index("coordinate")
+            coordinate = args[coordinate_index]
+
+        if len(coordinate) == 2:
+            coordinate = [coordinate[0], coordinate[1], 0.0]
+
+        if "coordinate" in kwargs:
+            kwargs["coordinate"] = coordinate
+        else:
+            args = list(args)
+            args[coordinate_index] = coordinate
+            args = tuple(args)
+
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
 def get_distance_between_coordinates(coordinate1: List[float], coordinate2: List[float]) -> float:
     """
     Get the distance between two coordinates.

tests/py/unit/fixtures.py

@@ -170,7 +170,7 @@
     "bulk": SI_CONVENTIONAL_CELL,
     "miller_indices": (0, 0, 1),
     "thickness": 1,
-    "vacuum": 1,
+    "vacuum": 5.0,
     "xy_supercell_matrix": [[1, 0], [0, 1]],
     "use_conventional_cell": True,
     "use_orthogonal_z": True,
@@ -211,69 +211,7 @@
     "_id": "",
     "metadata": {
         "boundaryConditions": {"type": "pbc", "offset": 0},
-        "build": {
-            "termination": "Si_P6/mmm_1",
-            "configuration": {
-                "type": "SlabConfiguration",
-                "bulk": {
-                    "name": "Si8",
-                    "basis": {
-                        "elements": [
-                            {"id": 0, "value": "Si"},
-                            {"id": 1, "value": "Si"},
-                            {"id": 2, "value": "Si"},
-                            {"id": 3, "value": "Si"},
-                            {"id": 4, "value": "Si"},
-                            {"id": 5, "value": "Si"},
-                            {"id": 6, "value": "Si"},
-                            {"id": 7, "value": "Si"},
-                        ],
-                        "coordinates": [
-                            {"id": 0, "value": [0.5, 0.0, 0.0]},
-                            {"id": 1, "value": [0.25, 0.25, 0.75]},
-                            {"id": 2, "value": [0.5, 0.5, 0.5]},
-                            {"id": 3, "value": [0.25, 0.75, 0.25]},
-                            {"id": 4, "value": [0.0, 0.0, 0.5]},
-                            {"id": 5, "value": [0.75, 0.25, 0.25]},
-                            {"id": 6, "value": [0.0, 0.5, 0.0]},
-                            {"id": 7, "value": [0.75, 0.75, 0.75]},
-                        ],
-                        "units": "crystal",
-                        "cell": [[5.468763846, 0.0, 0.0], [-0.0, 5.468763846, 0.0], [0.0, 0.0, 5.468763846]],
-                        "constraints": [],
-                        "labels": [],
-                    },
-                    "lattice": {
-                        "a": 5.468763846,
-                        "b": 5.468763846,
-                        "c": 5.468763846,
-                        "alpha": 90.0,
-                        "beta": 90.0,
-                        "gamma": 90.0,
-                        "units": {"length": "angstrom", "angle": "degree"},
-                        "type": "TRI",
-                        "vectors": {
-                            "a": [5.468763846, 0.0, 0.0],
-                            "b": [-0.0, 5.468763846, 0.0],
-                            "c": [0.0, 0.0, 5.468763846],
-                            "alat": 1,
-                            "units": "angstrom",
-                        },
-                    },
-                    "isNonPeriodic": False,
-                    "_id": "",
-                    "metadata": {"boundaryConditions": {"type": "pbc", "offset": 0}},
-                    "isUpdated": True,
-                },
-                "miller_indices": (0, 0, 1),
-                "thickness": 1,
-                "vacuum": 5.0,
-                "xy_supercell_matrix": [[1, 0], [0, 1]],
-                "use_conventional_cell": True,
-                "use_orthogonal_z": True,
-                "make_primitive": True,
-            },
-        },
+        "build": {"configuration": SI_SLAB_CONFIGURATION, "termination": "Si_P6/mmm_1"},
     },
     "isUpdated": True,
 }

tests/py/unit/test_tools_build_defect.py

@@ -107,7 +107,7 @@ def test_create_crystal_site_adatom():
 
     assert defect.basis.elements.values[-1] == "Si"
     assertion_utils.assert_deep_almost_equal(
-        # TO pass on GHA
+        # Adjusted expected value to pass tests on GHA due to slab generation differences between GHA and local
         [0.083333333, 0.458333333, 0.561569594],
         defect.basis.coordinates.values[-1],
     )

tests/py/unit/test_tools_build_grain_boundary.py

@@ -57,7 +57,7 @@ def test_slab_grain_boundary_builder():
         [0.0, 3.867, 0.0],
         [0.0, 0.0, 8.734],
     ]
-    # To pass on GHA
+    # Adjusted expected value to pass tests on GHA due to slab generation differences between GHA and local
     expected_coordinate_15 = [0.777190818, 0.0, 0.110688115]
 
     assert len(gb.basis.elements.values) == 32

tests/py/unit/test_tools_build_slab.py

@@ -19,5 +19,4 @@ def test_build_slab():
     )
     termination = get_terminations(slab_config)[0]
     slab = create_slab(slab_config, termination)
-    print(slab.to_json())
     assertion_utils.assert_deep_almost_equal(SI_SLAB, slab.to_json())