def test_minimize(self):
calculator = Sparrow('PM6')
calculator.set_elements(list(self.atoms.symbols))
calculator.set_positions(self.atoms.positions)
calculator.set_settings({
'molecular_charge': self.charge,
'spin_multiplicity': self.spin_multiplicity
})
energy1 = calculator.calculate_energy()
gradients1 = calculator.calculate_gradients()
opt_atoms, success = minimize(calculator=calculator,
atoms=self.atoms,
charge=self.charge,
spin_multiplicity=self.spin_multiplicity)
calculator.set_positions(opt_atoms.positions)
energy2 = calculator.calculate_energy()
gradients2 = calculator.calculate_gradients()
self.assertTrue(energy1 > energy2)
self.assertTrue(
np.sum(np.square(gradients1)) > np.sum(np.square(gradients2)))
self.assertTrue(np.all(gradients2 < 1E-3))
def test_minimize_fail(self):
calculator = Sparrow('PM6')
calculator.set_elements(list(self.atoms.symbols))
calculator.set_positions(self.atoms.positions)
calculator.set_settings({
'molecular_charge': self.charge,
'spin_multiplicity': self.spin_multiplicity
})
opt_atoms, success = minimize(
calculator=calculator,
atoms=self.atoms,
charge=self.charge,
spin_multiplicity=self.spin_multiplicity,
max_iter=1,
)
self.assertFalse(success)
def test_minimize_fixed(self):
calculator = Sparrow('PM6')
calculator.set_elements(list(self.atoms.symbols))
calculator.set_positions(self.atoms.positions)
calculator.set_settings({
'molecular_charge': self.charge,
'spin_multiplicity': self.spin_multiplicity
})
fixed_index = 2
opt_atoms, success = minimize(
calculator=calculator,
atoms=self.atoms,
charge=self.charge,
spin_multiplicity=self.spin_multiplicity,
fixed_indices=[fixed_index],
)
self.assertTrue(
np.all((self.atoms.positions -
opt_atoms.positions)[fixed_index] < 1E-6))