def test_mbar(self):
mbar = estimate_multi_temperature(self.energy_trajs,
self.temp_trajs,
self.dtrajs,
energy_unit='kT',
temp_unit='kT',
maxiter=50000,
maxerr=1.0E-13,
estimator='mbar')
validate_thermodynamics(self, mbar)
check_serialization(mbar)
def test_wham(self):
wham = estimate_multi_temperature(self.energy_trajs,
self.temp_trajs,
self.dtrajs,
energy_unit='kT',
temp_unit='kT',
maxiter=100000,
maxerr=1.0E-13,
estimator='wham')
validate_thermodynamics(self, wham)
check_serialization(wham)
def test_dtram2(self):
''' check we have the temperatures attribute for every estimated lag time'''
dtram = estimate_multi_temperature(self.energy_trajs,
self.temp_trajs,
self.dtrajs,
energy_unit='kT',
temp_unit='kT',
maxiter=50000,
maxerr=1.0E-10,
estimator='dtram',
lag=[10, 11])
for t in dtram:
assert hasattr(t, 'temperatures')
def test_dtram(self):
dtram = estimate_multi_temperature(self.energy_trajs,
self.temp_trajs,
self.dtrajs,
energy_unit='kT',
temp_unit='kT',
maxiter=50000,
maxerr=1.0E-10,
estimator='dtram',
lag=10)
validate_thermodynamics(self, dtram)
validate_kinetics(self, dtram)
check_serialization(dtram)
def test_tram(self):
tram = estimate_multi_temperature(self.energy_trajs,
self.temp_trajs,
self.dtrajs,
energy_unit='kT',
temp_unit='kT',
maxiter=10000,
maxerr=1.0E-10,
estimator='tram',
lag=10,
connectivity='reversible_pathways')
validate_thermodynamics(self, tram)
validate_kinetics(self, tram)
check_serialization(tram)
def test_multi_temperature_data():
req_keys = ('trajs', 'dtrajs', 'energy_trajs', 'temp_trajs', 'centers')
mt_data = get_multi_temperature_data()
for key in mt_data.keys():
assert key in req_keys
for key in req_keys:
assert key in mt_data
memm = estimate_multi_temperature(mt_data['energy_trajs'],
mt_data['temp_trajs'],
mt_data['dtrajs'],
energy_unit='kT',
temp_unit='kT',
reference_temperature=1.0,
estimator='dtram',
lag=[5],
maxiter=10000,
maxerr=1e-14)
assert memm.msm is not None
memm.msm.pcca(2)
pi = [memm.msm.pi[s].sum() for s in memm.msm.metastable_sets]
assert_allclose(pi, [0.3, 0.7], rtol=0.25, atol=0.1)