def test_define_lattice_from_file(self):
with patch('lattice_mc.init_lattice.lattice_from_sites_file'
) as mock_lattice_from_file:
mock_lattice_from_file.return_value = 'foo'
simulation = Simulation()
cell_lengths = np.array([1.0, 2.0, 3.0])
simulation.define_lattice_from_file('filename', cell_lengths)
self.assertEqual(simulation.lattice, 'foo')
mock_lattice_from_file.assert_called_with(
'filename', cell_lengths=cell_lengths)
def test_set_number_of_atoms_with_specific_sites(self):
simulation = Simulation()
simulation.lattice = Mock(spec=Lattice)
mock_atoms = [Mock(spec=Atom), Mock(spec=Atom)]
simulation.lattice.populate_sites = Mock(return_value=mock_atoms)
with patch('lattice_mc.species.Species') as mock_Species:
mock_Species.return_value = 'some atoms'
simulation.set_number_of_atoms(3, selected_sites=['A'])
self.assertEqual(
simulation.lattice.populate_sites.call_args[1]
['selected_sites'], ['A'])
def test_set_number_of_atoms(self):
simulation = Simulation()
simulation.lattice = Mock(spec=Lattice)
mock_atoms = [Mock(spec=Atom), Mock(spec=Atom)]
simulation.lattice.populate_sites = Mock(return_value=mock_atoms)
with patch('lattice_mc.species.Species') as mock_Species:
mock_Species.return_value = 'some atoms'
simulation.set_number_of_atoms(3)
self.assertEqual(simulation.number_of_atoms, 3)
self.assertEqual(simulation.atoms, 'some atoms')
mock_Species.assert_called_with(mock_atoms)
def test_run_with_equilibration_steps(self):
simulation = Simulation()
simulation.is_initialised = Mock(return_value=(True, None))
simulation.atoms = 'a'
simulation.lattice = Mock(spec=Lattice)
simulation.lattice.jump = Mock()
simulation.reset = Mock()
simulation.number_of_equilibration_jumps = 20
simulation.number_of_jumps = 30
simulation.run()
self.assertEqual(simulation.lattice.jump.call_count, 20 + 30)
self.assertEqual(simulation.reset.call_count, 1)
def test_is_initialised_fails_with_no_lattice(self):
simulation = Simulation()
simulation.atoms = 'foo'
simulation.number_of_jumps = 'bar'
simulation.lattice = None
with self.assertRaises(AttributeError):
simulation.is_initialised()
def test_simulation_is_initialised(self):
simulation = Simulation()
self.assertEqual(simulation.lattice, None)
self.assertEqual(simulation.number_of_atoms, None)
self.assertEqual(simulation.number_of_equilibration_jumps, 0)
self.assertEqual(simulation.number_of_jumps, None)
self.assertEqual(simulation.for_time, None)
self.assertEqual(simulation.number_of_atoms, None)
self.assertEqual(simulation.has_run, False)
def test_reset(self):
simulation = Simulation()
simulation.lattice = Mock(spec=Lattice)
simulation.atoms = Mock(spec=Species)
simulation.atoms.atoms = [Mock(spec=Atom), Mock(spec=Atom)]
simulation.reset()
self.assertEqual(simulation.lattice.reset.call_count, 1)
self.assertEqual(simulation.atoms.atoms[0].reset.call_count, 1)
self.assertEqual(simulation.atoms.atoms[1].reset.call_count, 1)
def test_run_for_time(self):
simulation = Simulation()
simulation.is_initialised = Mock(return_value=(True, None))
simulation.atoms = 'a'
simulation.lattice = Mock(spec=Lattice)
simulation.lattice.time = 0.0
def fake_jump_method():
simulation.lattice.time += 1.0
simulation.lattice.jump = fake_jump_method
simulation.run(for_time=10.0)
self.assertEqual(simulation.lattice.time, 10.0)
self.assertEqual(simulation.number_of_jumps, 10)
def test_collective_correlation(self):
s = Simulation()
self.assertEqual(s.collective_correlation, None)
def test_set_site_energies(self):
simulation = Simulation()
simulation.lattice = Mock(spec=Lattice)
simulation.lattice.set_site_energies = Mock()
simulation.set_site_energies('foo')
simulation.lattice.set_site_energies.assert_called_with('foo')
def test_set_nn_energy(self):
simulation = Simulation()
simulation.lattice = Mock(spec=Lattice)
simulation.lattice.set_nn_energy = Mock()
simulation.set_nn_energy('foo')
simulation.lattice.set_nn_energy.assert_called_with('foo')
def test_set_number_of_equilibration_jumps(self):
simulation = Simulation()
simulation.set_number_of_equilibration_jumps(32)
self.assertEqual(simulation.number_of_equilibration_jumps, 32)
def setUp(self):
self.simulation = Simulation()
self.simulation.has_run = True
def test_collective_diffusion_coefficient_per_atom(self):
s = Simulation()
self.assertEqual(s.collective_diffusion_coefficient_per_atom, None)
def test_run_raises_error_if_not_initialised(self):
simulation = Simulation()
simulation.is_initialised = Mock(side_effect=AttributeError('test'))
with self.assertRaises(AttributeError) as context:
simulation.run()
def test_tracer_diffusion_coefficient(self):
s = Simulation()
self.assertEqual(s.tracer_diffusion_coefficient, None)
def test_tracer_correlation(self):
s = Simulation()
self.assertEqual(s.tracer_correlation, None)