update: various cleaups

Exabyte-io · Oct 4, 2024 · 74f58e1 · 74f58e1
1 parent d46c197
commit 74f58e1
Show file tree

Hide file tree

Showing 5 changed files with 4 additions and 68 deletions.
diff --git a/src/py/mat3ra/made/tools/build/defect/builders.py b/src/py/mat3ra/made/tools/build/defect/builders.py
@@ -175,7 +175,6 @@ 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
         )

diff --git a/tests/py/unit/fixtures.py b/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,
 }

diff --git a/tests/py/unit/test_tools_build_defect.py b/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],
     )

diff --git a/tests/py/unit/test_tools_build_grain_boundary.py b/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

diff --git a/tests/py/unit/test_tools_build_slab.py b/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())