Vitor Hideyoshi
a5504b0435
- Replace manual property updates with @cached_property for total_mass, com, and inertia_tensor - Introduce invalidate_computed_properties decorator to auto-invalidate cached properties on atom changes - Vectorize distances_between_atoms, sizes_of_molecule, and minimum_distance calculations using numpy - Unify and clarify center of mass and standard orientation methods (move_center_of_mass_to_origin, rotate_to_standard_orientation) - Remove redundant or outdated code, improve typing and error handling - Update dependent files and tests to use new method names and behaviors
208 lines
5.4 KiB
Python
208 lines
5.4 KiB
Python
from diceplayer.environment import Atom, Molecule
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import numpy as np
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import numpy.testing as npt
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import unittest
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class TestMolecule(unittest.TestCase):
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def test_class_instantiation(self):
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mol = Molecule("test")
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self.assertIsInstance(mol, Molecule)
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def test_add_atom(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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self.assertEqual(len(mol.atom), 1)
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npt.assert_equal(mol.com, [1.0, 1.0, 1.0])
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def test_center_of_mass(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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npt.assert_equal(mol.com, [0.5, 0.5, 0.5])
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def test_center_of_mass_to_origin(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol.move_center_of_mass_to_origin()
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npt.assert_equal(mol.com, [0, 0, 0])
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def test_charges_and_dipole(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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actual_charge_dipole_array = mol.charges_and_dipole()
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expected_charge_dipole_array = [1.0, 0.0, 0.0, 0.0, 0.0]
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npt.assert_equal(actual_charge_dipole_array, expected_charge_dipole_array)
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def test_distances_between_atoms(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected = [
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[0.0, 1.73205081],
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[1.73205081, 0.0]
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]
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actual = mol.distances_between_atoms()
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npt.assert_almost_equal(
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expected, actual
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)
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def test_inertia_tensor(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected_inertia_tensor = [
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[1.00790, -0.50395, -0.50395],
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[-0.50395, 1.0079, -0.50395],
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[-0.50395, -0.50395, 1.0079],
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]
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actual_inertia_tensor = mol.inertia_tensor
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npt.assert_equal(expected_inertia_tensor, actual_inertia_tensor)
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def test_principal_axes(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected_evals, expected_evecs = (
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[0.0, 0.0, 0.0],
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[
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[1.0, 0.0, 0.0],
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[0.0, 1.0, 0.0],
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[0.0, 0.0, 1.0],
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],
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)
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evals, evecs = mol.principal_axes()
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npt.assert_equal(expected_evals, evals)
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npt.assert_equal(expected_evecs, evecs)
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def test_read_position(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected_position = mol.read_position()
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actual_position = mol.read_position()
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npt.assert_equal(expected_position, actual_position)
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def test_update_charges(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected_charges = [2.0]
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mol.update_charges(expected_charges)
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actual_charges = list(map(lambda a: a.chg, mol.atom))
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npt.assert_equal(expected_charges, actual_charges)
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def test_sizes_of_molecule(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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sizes = mol.sizes_of_molecule()
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expected_sizes = [0.0, 0.0, 0.0]
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npt.assert_equal(sizes, expected_sizes)
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def test_standard_orientation(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol.rotate_to_standard_orientation()
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expected_position = [0.0, 0.0, 0.0]
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self.assertEqual(mol.read_position().tolist(), expected_position)
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def test_translate(self):
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mol = Molecule("test")
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mol.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
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)
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new_mol = mol.translate(np.array([-1, -1, -1]))
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expected_position = [0.0, 0.0, 0.0]
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self.assertEqual(new_mol.read_position().tolist(), expected_position)
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def test_minimum_distance(self):
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mol1 = Molecule("test1")
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mol1.add_atom(
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Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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mol2 = Molecule("test2")
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mol2.add_atom(
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Atom(lbl=1, na=1, rx=1.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
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)
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expected_distance = 1.0
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actual_distance = mol1.minimum_distance(mol2)
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self.assertEqual(expected_distance, actual_distance)
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if __name__ == "__main__":
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unittest.main()
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