Test system (duartegroup#116)

Add tests for system.py

mlptrain/training/active.py

@@ -135,11 +135,11 @@ def train(
         md_program: (str) 'ASE' or 'OpenMM'
 
         pbc: (bool) If True, MLP-MD propagates with periodic boundary conditions.
-              The solvent should be therefore placed ina box and not sphere.
+              The solvent should be therefore placed in a box and not a sphere.
               The training data are still treated as clusters in
               electronic structure computations.
 
-        box_size: (List | None) Size of the box where MLP-MD propogated.
+        box_size: (List | None) Size of the box where MLP-MD propagated.
     """
     if md_program.lower() == 'openmm':
         if not isinstance(mlp, mlptrain.potentials.MACE):

tests/conftest.py

@@ -38,3 +38,22 @@ def h2o_configuration(h2o):
     config = system.random_configuration()
 
     return config
+
+
+@pytest.fixture
+def mg():
+    "Magnesium cation 2+"
+    atoms = [
+        Atom('Mg', 0.0, 0.0, 0.0),
+    ]
+    return mlt.Molecule(atoms=atoms, charge=+2, mult=1)
+
+
+@pytest.fixture
+def oh_radical():
+    "OH radiacal species"
+    atoms = [
+        Atom('O', 1.35670, 0.51322, 0.0),
+        Atom('H', 2.32670, 0.51322, 0.0),
+    ]
+    return mlt.Molecule(atoms=atoms, charge=0, mult=2)

tests/test_calculate.py

@@ -179,6 +179,7 @@ def test_method_and_keywords_invalid():
         _method_and_keywords('invalid_method')
 
 
+# @pytest.mark.xfail will be removed after autode update
 @pytest.mark.xfail
 def test_orca_keywords_success(set_config):
     """Test _orca_keywords retrieves the ORCA keywords from Config"""
@@ -195,6 +196,7 @@ def test_orca_keywords_no_config():
         _orca_keywords()
 
 
+# @pytest.mark.xfail will be removed after autode update
 @pytest.mark.xfail
 def test_gaussian_keywords_success(set_config):
     """Test _gaussian_keywords retrieves the Gaussian keywords from Config"""

tests/test_system.py

@@ -0,0 +1,96 @@
+import pytest
+import numpy as np
+import mlptrain as mlt
+from mlptrain.box import Box
+from mlptrain.configurations import Configuration, ConfigurationSet
+from autode.atoms import Atom
+
+
+@pytest.fixture
+def test_system(h2o):
+    """Create a sample system with a water molecule and a box."""
+    return mlt.System(h2o, box=Box([10, 10, 10]))
+
+
+@pytest.fixture
+def test_charged_system(mg):
+    """Create a sample system with a magnesium and a box."""
+    return mlt.System(mg, box=Box([10, 10, 10]))
+
+
+@pytest.fixture
+def test_radical_system(oh_radical):
+    """Create a sample system with a water molecule and a box."""
+    return mlt.System(oh_radical, box=Box([10, 10, 10]))
+
+
+def test_random_configuration(test_system):
+    """Test generating a random configuration for a system."""
+    config = test_system.random_configuration(min_dist=1.0)
+    assert len(config.atoms) == sum(
+        len(m.atoms) for m in test_system.molecules
+    )
+    assert test_system != config
+
+
+def test_random_configurations(test_system):
+    """Test generating multiple random configurations for a system."""
+    configs = test_system.random_configurations(num=5, min_dist=1.0)
+    assert isinstance(configs, ConfigurationSet)
+    assert len(configs) == 5
+    for config in configs:
+        assert isinstance(config, Configuration)
+        assert config != test_system
+
+
+def test_add_molecule(test_system, h2o):
+    """Test adding a single molecule to a system."""
+    initial_count = len(test_system.molecules)
+    test_system.add_molecule(h2o)
+    assert len(test_system.molecules) == initial_count + 1
+
+
+def test_add_multiple_molecules(test_system, h2o):
+    """Test adding multiple molecules to a system."""
+    initial_count = len(test_system.molecules)
+    test_system.add_molecules(h2o, num=3)
+    assert len(test_system.molecules) == initial_count + 3
+
+
+def test_charge_property(test_charged_system, mg):
+    """Test the system's total charge property."""
+    assert test_charged_system.charge == sum(
+        m.charge for m in test_charged_system.molecules
+    )
+
+
+def test_mult_property(test_radical_system, oh_radical):
+    """Test the system's total multiplicity property."""
+    expected_mult = 2
+    assert test_radical_system.mult == expected_mult
+
+
+def test_atoms_property(test_system):
+    """Test getting all atoms in the system."""
+    atoms = test_system.atoms
+    assert isinstance(atoms, list)
+    assert all(isinstance(atom, Atom) for atom in atoms)
+    total_atoms = sum(len(m.atoms) for m in test_system.molecules)
+    assert len(atoms) == total_atoms
+
+
+def test_unique_atomic_symbols_property(test_system):
+    """Test getting unique atomic symbols in the system."""
+    unique_symbols = test_system.unique_atomic_symbols
+    expected_symbols = set(
+        atom.label for mol in test_system.molecules for atom in mol.atoms
+    )
+    assert set(unique_symbols) == expected_symbols
+
+
+def test_shift_randomly_raises_runtimeerror_on_failure(test_system, h2o):
+    """Test that _shift_randomly raises RuntimeError after max attempts."""
+    with pytest.raises(RuntimeError):
+        test_system._shift_randomly(
+            h2o, coords=np.array([[0, 0, 0]]), min_dist=100
+        )