212 lines
5.5 KiB
Python
212 lines
5.5 KiB
Python
import numpy as np
|
|
|
|
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
|
|
)
|
|
|
|
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.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() |