Fix typo between abstract and concrete method class
@@ -336,8 +336,6 @@ class YankPhaseAnalyzer(ABC):
raise NotImplementedError("This class has not implemented this function")
-
-
# Static methods
@staticmethod
def get_decorrelation_time(timeseries_to_analyze):
@@ -638,7 +636,7 @@ class RepexPhase(YankPhaseAnalyzer):
u_n[iteration] = np.sum(np.diagonal(passed_timeseries[:, :, iteration]))
return u_n
- def prepare_MBAR_input_data(self, sampled_energy_matrix, unsampled_energy_matrix, nuse=0):
+ def _prepare_mbar_input_data(self, sampled_energy_matrix, unsampled_energy_matrix):
nstates, _, niterations = sampled_energy_matrix.shape
_, nunsampled, _ = unsampled_energy_matrix.shape
# Subsample data to obtain uncorrelated samples
@@ -788,7 +786,7 @@ class RepexPhase(YankPhaseAnalyzer):
unsampled_u_kln = self.remove_unequilibrated_data(unsampled_u_kln, number_equilibrated, -1)
u_kln = self.decorrelate_data(u_kln, g_t, -1)
unsampled_u_kln = self.decorrelate_data(unsampled_u_kln, g_t, -1)
- mbar_ukln, mbar_N_k = self.prepare_MBAR_input_data(u_kln, unsampled_u_kln)
+ mbar_ukln, mbar_N_k = self._prepare_mbar_input_data(u_kln, unsampled_u_kln)
self._create_mbar(mbar_ukln, mbar_N_k)
def analyze_phase(self, cutoff=0.05):
