update: add tests for edge passivation

Exabyte-io · Dec 6, 2024 · 9d92659 · 9d92659
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diff --git a/tests/py/unit/fixtures.py b/tests/py/unit/fixtures.py
@@ -492,6 +492,99 @@
     "isUpdated": True,
 }
 
+GRAPHENE_ZIGZAG_NANORIBBON_PASSIVATED = {
+    "name": "Graphene (Zigzag nanoribbon) H-passivated",
+    "basis": {
+        "elements": [
+            {"id": 0, "value": "C"},
+            {"id": 1, "value": "C"},
+            {"id": 2, "value": "C"},
+            {"id": 3, "value": "C"},
+            {"id": 4, "value": "C"},
+            {"id": 5, "value": "C"},
+            {"id": 6, "value": "C"},
+            {"id": 7, "value": "C"},
+            {"id": 8, "value": "C"},
+            {"id": 9, "value": "C"},
+            {"id": 10, "value": "C"},
+            {"id": 11, "value": "C"},
+            {"id": 12, "value": "C"},
+            {"id": 13, "value": "C"},
+            {"id": 14, "value": "C"},
+            {"id": 15, "value": "C"},
+            {"id": 16, "value": "H"},
+            {"id": 17, "value": "H"},
+            {"id": 18, "value": "H"},
+            {"id": 19, "value": "H"},
+            {"id": 20, "value": "H"},
+            {"id": 21, "value": "H"},
+            {"id": 22, "value": "H"},
+            {"id": 23, "value": "H"},
+        ],
+        "coordinates": [
+            {"id": 0, "value": [0.062499937, 0.366666681, 0.5]},
+            {"id": 1, "value": [0.312499937, 0.366666681, 0.5]},
+            {"id": 2, "value": [0.187500062, 0.433333286, 0.5]},
+            {"id": 3, "value": [0.187499937, 0.566666695, 0.5]},
+            {"id": 4, "value": [0.062500062, 0.6333333, 0.5]},
+            {"id": 5, "value": [0.562499937, 0.366666681, 0.5]},
+            {"id": 6, "value": [0.437500062, 0.433333286, 0.5]},
+            {"id": 7, "value": [0.437499937, 0.566666695, 0.5]},
+            {"id": 8, "value": [0.312500062, 0.6333333, 0.5]},
+            {"id": 9, "value": [0.812499938, 0.366666681, 0.5]},
+            {"id": 10, "value": [0.687500062, 0.433333286, 0.5]},
+            {"id": 11, "value": [0.687499937, 0.566666695, 0.5]},
+            {"id": 12, "value": [0.562500062, 0.6333333, 0.5]},
+            {"id": 13, "value": [0.937500063, 0.433333286, 0.5]},
+            {"id": 14, "value": [0.937499937, 0.566666695, 0.5]},
+            {"id": 15, "value": [0.812500063, 0.6333333, 0.5]},
+            {"id": 16, "value": [0.062500067, 0.228137674, 0.5]},
+            {"id": 17, "value": [0.312500067, 0.228137674, 0.5]},
+            {"id": 18, "value": [0.062499932, 0.771862307, 0.5]},
+            {"id": 19, "value": [0.562500067, 0.228137674, 0.5]},
+            {"id": 20, "value": [0.312499932, 0.771862307, 0.5]},
+            {"id": 21, "value": [0.812500068, 0.228137674, 0.5]},
+            {"id": 22, "value": [0.562499932, 0.771862307, 0.5]},
+            {"id": 23, "value": [0.812499933, 0.771862307, 0.5]},
+        ],
+        "units": "crystal",
+        "cell": [[9.869164, 0.0, 0.0], [-0.0, 10.683683, 0.0], [0.0, 0.0, 20.0]],
+        "labels": [],
+    },
+    "lattice": {
+        "a": 9.869164,
+        "b": 10.683683422,
+        "c": 20.0,
+        "alpha": 90.0,
+        "beta": 90.0,
+        "gamma": 90.0,
+        "units": {"length": "angstrom", "angle": "degree"},
+        "type": "TRI",
+        "vectors": {
+            "a": [9.869164, 0.0, 0.0],
+            "b": [-0.0, 10.683683422, 0.0],
+            "c": [0.0, 0.0, 20.0],
+            "alat": 1,
+            "units": "angstrom",
+        },
+    },
+    "isNonPeriodic": False,
+    "_id": "",
+    "metadata": {
+        "boundaryConditions": {"type": "pbc", "offset": 0},
+        "build": {
+            "configuration": {
+                "type": "PassivationConfiguration",
+                "slab": GRAPHENE_ZIGZAG_NANORIBBON,
+                "passivant": "H",
+                "bond_length": 1.48,
+                "surface": "both",
+            }
+        },
+    },
+    "isUpdated": True,
+}
+
 
 GRAPHENE_NICKEL_INTERFACE = {
     "name": "C2(001)-Ni4(111), Interface, Strain 0.105pct",

diff --git a/tests/py/unit/test_tools_build_passivation.py b/tests/py/unit/test_tools_build_passivation.py
@@ -1,9 +1,15 @@
 from mat3ra.made.material import Material
-from mat3ra.made.tools.build.passivation.builders import SurfacePassivationBuilder, SurfacePassivationBuilderParameters
+from mat3ra.made.tools.build.passivation import get_unique_coordination_numbers
+from mat3ra.made.tools.build.passivation.builders import (
+    CoordinationBasedPassivationBuilder,
+    CoordinationBasedPassivationBuilderParameters,
+    SurfacePassivationBuilder,
+    SurfacePassivationBuilderParameters,
+)
 from mat3ra.made.tools.build.passivation.configuration import PassivationConfiguration
 from mat3ra.utils import assertion as assertion_utils
 
-from .fixtures import SI_SLAB, SI_SLAB_PASSIVATED
+from .fixtures import GRAPHENE_ZIGZAG_NANORIBBON, GRAPHENE_ZIGZAG_NANORIBBON_PASSIVATED, SI_SLAB, SI_SLAB_PASSIVATED
 
 
 def test_passivate_surface():
@@ -13,3 +19,21 @@ def test_passivate_surface():
     )
     passivated_material = builder.get_material(config)
     assertion_utils.assert_deep_almost_equal(SI_SLAB_PASSIVATED, passivated_material.to_json())
+
+
+def test_get_unique_coordination_numbers():
+    config = PassivationConfiguration(
+        slab=Material(GRAPHENE_ZIGZAG_NANORIBBON), passivant="H", bond_length=1.48, surface="both"
+    )
+    unique_coordination_numbers = get_unique_coordination_numbers(config, cutoff=3.0)
+    assert unique_coordination_numbers == [2, 3]
+
+
+def test_passivate_edge():
+    config = PassivationConfiguration(slab=Material(GRAPHENE_ZIGZAG_NANORIBBON), passivant="H", bond_length=1.48)
+    params = CoordinationBasedPassivationBuilderParameters(
+        shadowing_radius=2.5, coordination_threshold=2, bonds_to_passivate=1
+    )
+    builder = CoordinationBasedPassivationBuilder(build_parameters=params)
+    passivated_material = builder.get_material(config)
+    assertion_utils.assert_deep_almost_equal(GRAPHENE_ZIGZAG_NANORIBBON_PASSIVATED, passivated_material.to_json())