def test_SurvivalProbability_zeroMolecules(universe):
# no atom IDs found
with patch.object(universe, 'select_atoms',
return_value=Mock(ids=[])) as select_atoms_mock:
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, start=3, stop=7, verbose=True)
assert all(np.isnan(sp.sp_timeseries[1:]))
def test_SurvivalProbability_stepEqualDtMax(universe):
with patch.object(universe, 'select_atoms',
return_value=Mock(ids=(1, ))) as select_atoms_mock:
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=4, step=5, stop=10, verbose=True)
# all frames from 0, with 9 inclusive
assert_equal(select_atoms_mock.call_count, 10)
def test_SurvivalProbability_alwaysPresent(universe):
# always the same atom IDs found, 7 and 8
with patch.object(universe, 'select_atoms',
return_value=Mock(ids=[7, 8])) as select_atoms_mock:
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, start=0, stop=7, verbose=True)
assert all(np.equal(sp.sp_timeseries, 1))
def test_SurvivalProbability_definedTaus(universe):
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9, 8, 7), (8, 7, 6), (7, 6, 5), (6, 5, 4), (5, 4, 3), (4, 3, 2), (3, 2, 1)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop()) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, start=0, stop=6)
assert_almost_equal(sp.sp_timeseries, [2 / 3.0, 1 / 3.0, 0])
def test_SurvivalProbability_stepLargerThanDtmax(universe):
# Testing if the frames are skipped correctly
with patch.object(universe, 'select_atoms',
return_value=Mock(ids=(1, ))) as select_atoms_mock:
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=2, step=5, stop=10, verbose=True)
assert_equal(sp.sp_timeseries, [1, 1, 1])
# with tau_max=2 for all the frames we only read 6 of them
# this is because the frames which are not used are skipped, and therefore 'select_atoms'
assert universe.trajectory.n_frames > 6
assert_equal(select_atoms_mock.call_count, 6)
def test_SurvivalProbability_intermittency2lacking(universe):
"""
If an atom is not present for more than 2 consecutive frames, it is considered to have left the region.
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9, ), (), (), (), (9, ), (), (), (), (9, )]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop(
)) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, stop=8, verbose=True, intermittency=2)
assert_almost_equal(sp.sp_timeseries, [0, 0, 0])
def test_SurvivalProbability_intermittency1and2(universe):
"""
Intermittency of 2 means that we still count an atom if it is not present for up to 2 consecutive frames,
but then returns at the following step.
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(9, 8), (), (8, ), (9, ), (8, ), (), (9, 8), (), (8, ), (9, 8)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop(
)) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=3, stop=10, verbose=True, intermittency=2)
assert all(x == {9, 8} for x in sp._intermittent_selected_ids)
assert_almost_equal(sp.sp_timeseries, [1, 1, 1, 1])
def test_SurvivalProbability_intermittency1_step5_noSkipping(universe):
"""
Step leads to skipping frames if (tau_max + 1) + (intermittency * 2) < step.
No frames should be skipped.
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(2, 3), (3, ), (2, 3), (3, ), (2, ), (3, ), (2, 3), (3, ),
(2, 3), (2, 3)]
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop(
)) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=2, stop=10, verbose=True, intermittency=1, step=5)
assert all((x == {2, 3} for x in sp._intermittent_selected_ids))
assert_almost_equal(sp.sp_timeseries, [1, 1, 1])
def test_SurvivalProbability_intermittency1_step5_Skipping(universe):
"""
Step leads to skipping frames if (tau_max + 1) * (intermittency * 2) < step.
In this case one frame will be skipped per window.
"""
with patch.object(universe, 'select_atoms') as select_atoms_mock:
ids = [(1, ), (), (1, ), (), (1, ), (), (1, ), (), (1, ), (1, )]
beforepopsing = len(ids) - 2
select_atoms_mock.side_effect = lambda selection: Mock(ids=ids.pop(
)) # atom IDs fed set by set
sp = waterdynamics.SurvivalProbability(universe, "")
sp.run(tau_max=1, stop=10, verbose=True, intermittency=1, step=5)
assert all((x == {1} for x in sp._intermittent_selected_ids))
assert len(sp._selected_ids) == beforepopsing
assert_almost_equal(sp.sp_timeseries, [1, 1])
def test_SurvivalProbability_t0Ignored(universe_prot):
sp = waterdynamics.SurvivalProbability(universe_prot, SELECTION3, 3, 10, 4)
sp.run()
assert_almost_equal(sp.timeseries, [1.0, 0.391, 0.292, 0.261], decimal=3)
def test_SurvivalProbability(universe_prot):
sp = waterdynamics.SurvivalProbability(universe_prot, SELECTION3, 0, 10, 4)
sp.run()
assert_almost_equal(sp.timeseries, [1.0, 0.354, 0.267, 0.242], decimal=3)
def test_SurvivalProbability_zeroMolecules(universe):
sp_zero = waterdynamics.SurvivalProbability(universe, SELECTION2, 0, 6, 3)
sp_zero.run()
assert_almost_equal(sp_zero.timeseries[1], 0.0)
