Update/SOF-7461 Update: various cleanups #165
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src/py/mat3ra/made/tools/analyze.py
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| @@ -492,6 +492,8 @@ def get_local_extremum_atom_index( | |||
| Returns: | |||
| int: id of the atom with the minimum or maximum z-coordinate. | |||
| """ | |||
| if len(coordinate) == 2: | |||
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This should be handled before invoking the function
| @@ -174,7 +175,11 @@ 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 = get_atomic_coordinates_extremum(material, use_cartesian_coordinates=False) | |||
tests/py/unit/fixtures.py
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| "configuration": SI_SLAB_CONFIGURATION, | ||
| "termination": "Si_P4/mmm_1", | ||
| "termination": "Si_P6/mmm_1", | ||
| "configuration": { |
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Let's keep SI_SLAB_CONFIGURATION
| @@ -109,7 +107,9 @@ def test_create_crystal_site_adatom(): | |||
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|
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| assert defect.basis.elements.values[-1] == "Si" | |||
| assertion_utils.assert_deep_almost_equal( | |||
| [0.083333333, 0.458333333, 0.352272727], defect.basis.coordinates.values[-1] | |||
| # TO pass on GHA | |||
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| ] | ||
| expected_coordinate_15 = [0.777190818, 0.0, 0.083333333] | ||
| # To pass on GHA |
| xy_supercell_matrix=[[1, 0], [0, 1]], | ||
| use_orthogonal_z=True, | ||
| make_primitive=True, | ||
| ) | ||
| termination = get_terminations(slab_config)[0] | ||
| slab = create_slab(slab_config, termination) | ||
| print(slab.to_json()) |
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| @@ -42,6 +42,35 @@ def wrapper(*args, **kwargs): | |||
| return wrapper | |||
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| 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]. | |||
timurbazhirov
approved these changes
Oct 5, 2024
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update functions in modify to reflect the type of operand - material, interface - as the first or last word in the name feature/SOF-7426
Setup logging function(s) per https://github.com/Exabyte-io/made/pull/163/files#diff-e4a26d8b67b5aeea2b22353665f197977c0e02fc72c85eaf083509447df8bf11R316
create_xxx in every init alongside imports of configs, builders and params
Functionality:
Use local max z detection in Adatom placement (to place on terrace or non-orthogonal surface)
Hetero material island