Implements More Tests and Begins Dice Refactor Implementation

tests/shared/environment/test_molecule.py

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+from diceplayer.shared.environment.molecule import Molecule
+from diceplayer.shared.environment.atom import Atom
+
+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., 1., 1.])
+
+    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, [.5, .5, .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.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_distance_between_atoms = [[1.73205081], [1.73205081]]
+        actual_distance_between_atoms = mol.distances_between_atoms()
+
+        npt.assert_almost_equal(
+            expected_distance_between_atoms,
+            actual_distance_between_atoms
+        )
+
+    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.], [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]
+
+        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.]
+        mol.update_charges(expected_charges)
+
+        actual_charges = list(map(lambda a: a.chg, mol.atom))
+
+        npt.assert_equal(
+            expected_charges,
+            actual_charges
+        )