Test extxyz file

tests/test_abstract_model.py

@@ -0,0 +1,107 @@
+import pytest
+
+from io import StringIO
+from ase.io import read
+import numpy as np
+
+from abcd.model import AbstractModel
+
+
+@pytest.fixture
+def extxyz_file():
+    return StringIO(
+        """2
+        Properties=species:S:1:pos:R:3:forces:R:3 energy=-1 pbc="F T F"
+        Si  0.0  0.0  0.0  0.4  0.6  -0.4
+        Si  0.0  0.0  0.0  -0.1  -0.5  -0.6
+        """
+    )
+
+
+def test_from_atoms(extxyz_file):
+    """Test extracting data from ASE Atoms object."""
+    expected_forces = np.array([[0.4, 0.6, -0.4], [-0.1, -0.5, -0.6]])
+    expected_stress = np.array([-1.0, -1.0, -1.0, -2.1, 2.0, 1.8])
+
+    atoms = read(extxyz_file, format="extxyz")
+    atoms.calc.results["stress"] = expected_stress
+    data = AbstractModel.from_atoms(atoms)
+
+    # Test info
+    info_keys = {
+        "pbc",
+        "n_atoms",
+        "cell",
+        "formula",
+        "calculator_name",
+        "calculator_parameters",
+    }
+    assert info_keys == set(data.info_keys)
+    assert data["pbc"] == [False, True, False]
+    assert data["n_atoms"] == 2
+    assert len(data["cell"]) == 3
+    assert all(arr == [0.0, 0.0, 0.0] for arr in data["cell"])
+    assert data["formula"] == "Si2"
+
+    # Test arrays
+    assert {"numbers", "positions"} == set(data.arrays_keys)
+
+    # Test results
+    assert {"energy", "stress", "forces"} == set(data.results_keys)
+    assert data["energy"] == -1
+    assert data["forces"] == pytest.approx(expected_forces)
+    assert data["stress"] == pytest.approx(expected_stress)
+
+    # Test derived
+    derived_keys = {
+        "elements",
+        "username",
+        "uploaded",
+        "modified",
+        "volume",
+        "hash",
+        "hash_structure",
+    }
+    assert derived_keys == set(data.derived_keys)
+
+
+def test_from_atoms_no_calc(extxyz_file):
+    """Test extracting data from ASE Atoms object without results."""
+    expected_stress = np.array([-1.0, -1.0, -1.0, -2.1, 2.0, 1.8])
+
+    atoms = read(extxyz_file, format="extxyz")
+    atoms.calc.results["stress"] = expected_stress
+    data = AbstractModel.from_atoms(atoms, store_calc=False)
+
+    # Test info
+    assert {"pbc", "n_atoms", "cell", "formula"} == set(data.info_keys)
+    assert data["pbc"] == [False, True, False]
+    assert data["n_atoms"] == 2
+    assert len(data["cell"]) == 3
+    assert all(arr == [0.0, 0.0, 0.0] for arr in data["cell"])
+    assert data["formula"] == "Si2"
+
+    # Test arrays
+    assert {"numbers", "positions"} == set(data.arrays_keys)
+
+    # Test results
+    results_keys = {
+        "energy",
+        "forces",
+        "stress",
+        "calculator_name",
+        "calculator_parameters",
+    }
+    assert all(key not in data for key in results_keys)
+
+    # Test derived
+    derived_keys = {
+        "elements",
+        "username",
+        "uploaded",
+        "modified",
+        "volume",
+        "hash",
+        "hash_structure",
+    }
+    assert derived_keys == set(data.derived_keys)