Store whole u_n for notebook, but indicate appropriate equilibration time
@@ -440,12 +440,12 @@ class ExperimentAnalyzer(object):
"*something* to analyze.")
self._n_discarded = 0
- self.u_ns[phase_name] = analyzer.get_effective_energy_timeseries()[t0:]
+ self.u_ns[phase_name] = analyzer.get_effective_energy_timeseries()[1:]
# Timeseries statistics
i_t, g_i, n_effective_i = multistate.get_equilibration_data_per_sample(self.u_ns[phase_name])
n_effective_max = n_effective_i.max()
i_max = n_effective_i.argmax()
- n_equilibration = i_t[i_max]
+ n_equilibration = i_t[i_max] + t0
g_t = g_i[i_max]
self.Neff_maxs[phase_name] = n_effective_max
self.nequils[phase_name] = n_equilibration
