Add test for creation of alchemical ions.

tests/runner/test_alchemical_ions.py

@@ -0,0 +1,31 @@
+import math
+
+from somd2.runner import Runner
+
+
+def test_alchemical_ions(ethane_methanol):
+    """Ensure that alchemical ions are added correctly."""
+
+    # Clone the system.
+    mols = ethane_methanol.clone()
+
+    # Helper function to return the charge difference between the end states.
+    def charge_difference(mols):
+        from sire import morph
+
+        reference = morph.link_to_reference(mols)
+        perturbed = morph.link_to_perturbed(mols)
+
+        return (perturbed.charge() - reference.charge()).value()
+
+    # Add 10 Cl- ions.
+    new_mols = Runner._create_alchemical_ions(mols, 10)
+
+    # Make sure the charge difference is correct.
+    assert math.isclose(charge_difference(new_mols), -10.0, rel_tol=1e-6)
+
+    # Add 10 Na+ ions.
+    new_mols = Runner._create_alchemical_ions(mols, -10)
+
+    # Make sure the charge difference is correct.
+    assert math.isclose(charge_difference(new_mols), 10.0, rel_tol=1e-6)