add tests for cluster_point_group

python/libcasm/xtal/cluster_point_group.py

@@ -925,9 +925,7 @@ def issue_warning_if_origin_is_not_center_of_geometry(
         tol,
         tol,
     ):
-        import warnings
-
-        warnings.warn(
+        print(
             "WARNING: Geometric center of mass of the molecule is not at origin. Shifting it to origin. If you are working on the molecule further please shift it's geometric center of mass to origin."
         )
     return None

python/tests/test_cluster_point_group.py

@@ -0,0 +1,111 @@
+import os
+import pytest
+from typing import Tuple
+import libcasm.xtal as xtal
+
+
+def supply_molecules_and_expected_point_group_operations(
+    session_shared_datadir: str, molecule_name: str
+) -> Tuple[xtal.Occupant, str, float]:
+    """Supplies a list of some general molecules on which
+    you can test the point group code
+
+    Parameters
+    ----------
+    pytest_root_dir : str
+    molecule_name : str
+
+    Returns
+    -------
+    Tuple[xtal.Occupant, int, tol]
+        xtal.Occupant object, number of point group operations expected,
+        tolerance of comparisions
+
+
+    """
+    molecules_dir = os.path.join(session_shared_datadir, "input_molecules")
+
+    # For ammonia, you will have 6 point group operations
+    if molecule_name == "ammonia":
+        with open(os.path.join(molecules_dir, "ammonia.xyz"), "r") as f:
+            xyz_string = f.read()
+        return (
+            xtal.Occupant.from_xyz_string(xyz_string),
+            6,
+            1e-3,
+        )
+
+    # For benzene, you will have 24 point group operations
+    elif molecule_name == "benzene":
+        with open(os.path.join(molecules_dir, "benzene.xyz"), "r") as f:
+            xyz_string = f.read()
+        return (
+            xtal.Occupant.from_xyz_string(xyz_string),
+            24,
+            1e-3,
+        )
+
+    # For ethane, you will have 12 point group operations
+    elif molecule_name == "ethane":
+        with open(os.path.join(molecules_dir, "ethane.xyz"), "r") as f:
+            xyz_string = f.read()
+        return (
+            xtal.Occupant.from_xyz_string(xyz_string),
+            12,
+            1e-2,
+        )
+
+    # For square, you will have 16 point group operations
+    elif molecule_name == "square":
+        with open(os.path.join(molecules_dir, "square.xyz"), "r") as f:
+            xyz_string = f.read()
+        return (
+            xtal.Occupant.from_xyz_string(xyz_string),
+            16,
+            1e-5,
+        )
+
+    # For water, you will have 4 point group operations
+    elif molecule_name == "water":
+        with open(os.path.join(molecules_dir, "water.xyz"), "r") as f:
+            xyz_string = f.read()
+        return (
+            xtal.Occupant.from_xyz_string(xyz_string),
+            4,
+            1e-5,
+        )
+
+    else:
+        raise RuntimeError("Unknown molecule type")
+
+
+@pytest.mark.parametrize(
+    "molecule",
+    [
+        "ammonia",
+        "benzene",
+        "ethane",
+        "square",
+        "water",
+    ],
+)
+def test_point_group_molecule(session_shared_datadir: str, molecule: str):
+    """Tests the point group of molecule for the given code
+    Currently tests against the hard coded number of point
+    group operations a molecule should have.
+
+    Parameters
+    ----------
+    pytest_root_dir : str
+    molecule: str
+    """
+    (
+        occupant,
+        expected_number_of_pg_operations,
+        tol,
+    ) = supply_molecules_and_expected_point_group_operations(
+        session_shared_datadir, molecule
+    )
+
+    point_group = xtal.cluster_point_group(occupant, tol)
+    assert len(point_group) == expected_number_of_pg_operations