def test_keywordonly_arguments(self):
def dum(x):
return x
with pytest.raises(TypeError):
boot.mix_and_bootstrap([1], [2], dum, dum, 10000) # pylint: disable=too-many-function-args
def test_valueerror(self):
with pytest.raises(ValueError):
boot.mix_and_bootstrap([1], [2], num_iterations=0)
with pytest.raises(ValueError):
boot.mix_and_bootstrap([1], [2], num_iterations=-1)
def vDSSB_jarzynski_error_propagation(works_1,
works_2,
*,
temperature=298.15,
boltzmann_kappa=0.001985875,
num_iterations=10000):
"""get STD of the Jarzynki free energy obtained by convolution of bound and unbound work vDSSB
starting from the bound and unbound work values calculates the STD of the Jarzynski
free energy estimate (if you use the vDSSB method)
it uses bootstrapping, can be very time and memory consuming
Parameters
-----------
works_1 : numpy.array
the first numpy array of the work values
works_2 : numpy.array
the second numpy array of the work values
temperature : float, optional
the temperature in Kelvin at which the non equilibrium simulation
has been done, default 298.15 K
boltzmann_kappa : float
the Boltzmann constant, the dafault is 0.001985875 kcal/(mol⋅K)
and if you keep it the `works` shall be in Kcal
num_iterations : ins, optional, default=10000
the number of bootstrapping iterations (time and memory consuming)
Returns
----------
STD, mean : float, float
the STD of the Jarzynski estimate and it's bootstrapped mean value
Notes
-----------
it uses the `jarzynski_free_energy` present in this module, it uses bootstrapping,
will take for granted that you mixed the work values with
`PythonFSDAM.combine_works.combine_non_correlated_works` and uses the
`PythonFSDAM.bootstrapping.mix_and_bootstrap` function to do the bootstrapping
"""
helper_obj = _vDSSBJarzynskiErrorPropagationHelperClass(
temperature=temperature, boltzmann_kappa=boltzmann_kappa)
out_mean, out_std = boot.mix_and_bootstrap(
works_1,
works_2,
mixing_function=combine.combine_non_correlated_works,
stat_function=helper_obj.calculate_jarzynski,
num_iterations=num_iterations)
return out_std, out_mean
def test_non_correlated_mixing_and_jarzynski(self):
values_1 = np.array([-1, -2, -3, 1, 2, 3])
values_2 = np.array([-4, -5, -6, 4, 5, 6])
#calculated in a previous run
expected_mean = -6.463986
#expected_std = 1.519654
out_mean, _ = boot.mix_and_bootstrap(
values_1,
values_2,
mixing_function=combine.combine_non_correlated_works,
stat_function=free.jarzynski_free_energy,
num_iterations=10000)
assert np.testing.assert_allclose(out_mean, expected_mean,
rtol=0.01) is None
def test_works(self, mocker):
values_1 = np.array([1, 2, 3])
values_2 = np.array([4, 5, 6])
m_mixing = mock.MagicMock()
m_stat = mock.MagicMock()
m_pool = mocker.patch('multiprocessing.pool.Pool')
m_pool_enter = mock.MagicMock()
m_pool_enter.return_value.starmap_async.return_value.get.return_value = [
1., 2., 3.
]
m_pool.return_value.__enter__.return_value = m_pool_enter
m_array = mocker.patch('numpy.array', return_value=1.)
m_mean = mocker.patch('numpy.mean', return_value=1.)
m_std = mocker.patch('numpy.std', return_value=2.)
mocker.patch.dict('os.environ')
out_mean, out_std = boot.mix_and_bootstrap(values_1,
values_2,
mixing_function=m_mixing,
stat_function=m_stat,
num_iterations=1,
n_threads=2)
assert out_mean == 1.
assert out_std == 2.
assert m_pool.call_args[0][0] == 2
m_stat.assert_not_called()
m_array.assert_called_once()
m_mean.assert_called_once()
m_std.assert_called_once()
def test_with_helper_class(self):
helper_obj = Helper(temperature=100., boltzmann_kappa=0.1)
values_1 = np.array([-1, -2, -3, 1, 2, 3])
values_2 = np.array([-4, -5, -6, 4, 5, 6])
#calculated in a previous run
expected_mean = -1.20363
#expected_std = 2.190256
out_mean, _ = boot.mix_and_bootstrap(
values_1,
values_2,
mixing_function=combine.combine_non_correlated_works,
stat_function=helper_obj.calculate_jarzynski,
num_iterations=10000)
assert np.testing.assert_allclose(out_mean, expected_mean,
rtol=0.07) is None
def test_with_simple_function(self):
values_1 = np.array([1, 2, 3])
values_2 = np.array([4, 5, 6])
expected_mean = np.mean(values_1 + values_2)
expected_std = np.std(values_1 + values_2)
out_mean, out_std = boot.mix_and_bootstrap(
values_1,
values_2,
mixing_function=simple_mix,
stat_function=dummy_calculation,
num_iterations=10000)
assert np.testing.assert_allclose(out_mean, expected_mean,
rtol=0.003) is None
#this assertion may fail
assert np.testing.assert_allclose(out_std, expected_std,
rtol=0.6) is None