refactor: replace Logger with RunLogger and streamline logging setup

tests/environment/test_molecule.py

@@ -0,0 +1,202 @@
+from diceplayer.environment import Atom, Molecule
+
+import numpy as np
+import numpy.testing as npt
+
+import unittest
+
+
+class TestMolecule(unittest.TestCase):
+    def test_class_instantiation(self):
+        mol = Molecule("test")
+
+        self.assertIsInstance(mol, Molecule)
+
+    def test_add_atom(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        self.assertEqual(len(mol.atom), 1)
+        npt.assert_equal(mol.com, [1.0, 1.0, 1.0])
+
+    def test_center_of_mass(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        npt.assert_equal(mol.com, [0.5, 0.5, 0.5])
+
+    def test_center_of_mass_to_origin(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        mol.move_center_of_mass_to_origin()
+
+        npt.assert_equal(mol.com, [0, 0, 0])
+
+    def test_charges_and_dipole(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        actual_charge_dipole_array = mol.charges_and_dipole()
+
+        expected_charge_dipole_array = [1.0, 0.0, 0.0, 0.0, 0.0]
+
+        npt.assert_equal(actual_charge_dipole_array, expected_charge_dipole_array)
+
+    def test_distances_between_atoms(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected = [[0.0, 1.73205081], [1.73205081, 0.0]]
+        actual = mol.distances_between_atoms()
+
+        npt.assert_almost_equal(expected, actual)
+
+    def test_inertia_tensor(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected_inertia_tensor = [
+            [1.00790, -0.50395, -0.50395],
+            [-0.50395, 1.0079, -0.50395],
+            [-0.50395, -0.50395, 1.0079],
+        ]
+
+        actual_inertia_tensor = mol.inertia_tensor
+
+        npt.assert_equal(expected_inertia_tensor, actual_inertia_tensor)
+
+    def test_principal_axes(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected_evals, expected_evecs = (
+            [0.0, 0.0, 0.0],
+            [
+                [1.0, 0.0, 0.0],
+                [0.0, 1.0, 0.0],
+                [0.0, 0.0, 1.0],
+            ],
+        )
+
+        evals, evecs = mol.principal_axes()
+
+        npt.assert_equal(expected_evals, evals)
+        npt.assert_equal(expected_evecs, evecs)
+
+    def test_read_position(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected_position = mol.read_position()
+
+        actual_position = mol.read_position()
+
+        npt.assert_equal(expected_position, actual_position)
+
+    def test_update_charges(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected_charges = [2.0]
+        mol.update_charges(expected_charges)
+
+        actual_charges = list(map(lambda a: a.chg, mol.atom))
+
+        npt.assert_equal(expected_charges, actual_charges)
+
+    def test_sizes_of_molecule(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        sizes = mol.sizes_of_molecule()
+
+        expected_sizes = [0.0, 0.0, 0.0]
+
+        npt.assert_equal(sizes, expected_sizes)
+
+    def test_standard_orientation(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        mol.rotate_to_standard_orientation()
+
+        expected_position = [0.0, 0.0, 0.0]
+
+        self.assertEqual(mol.read_position().tolist(), expected_position)
+
+    def test_translate(self):
+        mol = Molecule("test")
+
+        mol.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        new_mol = mol.translate(np.array([-1, -1, -1]))
+
+        expected_position = [0.0, 0.0, 0.0]
+
+        self.assertEqual(new_mol.read_position().tolist(), expected_position)
+
+    def test_minimum_distance(self):
+        mol1 = Molecule("test1")
+        mol1.add_atom(
+            Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        mol2 = Molecule("test2")
+        mol2.add_atom(
+            Atom(lbl=1, na=1, rx=1.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
+        )
+
+        expected_distance = 1.0
+
+        actual_distance = mol1.minimum_distance(mol2)
+
+        self.assertEqual(expected_distance, actual_distance)
+
+
+if __name__ == "__main__":
+    unittest.main()