Added fast ability to the ged_equilibration data
@@ -349,10 +349,11 @@ class YankPhaseAnalyzer(ABC):
return n_equilibration, g_t, n_effective_max
@staticmethod
- def get_equilibration_data_per_sample(timeseries_to_analyze, nskip=1):
+ def get_equilibration_data_per_sample(timeseries_to_analyze, fast=True, nskip=1):
"""
Compute the correlation time and n_effective per sample.
This is exactly what timeseries.detectEquilibration does, but returns the per sample data
+ See the timeseries.detectEquilibration function for full documentaiton
"""
A_t = timeseries_to_analyze
T = A_t.size
@@ -360,7 +361,7 @@ class YankPhaseAnalyzer(ABC):
Neff_t = np.ones([T - 1], np.float32)
for t in range(0, T - 1, nskip):
try:
- g_t[t] = timeseries.statisticalInefficiency(A_t[t:T])
+ g_t[t] = timeseries.statisticalInefficiency(A_t[t:T], fast=fast)
except:
g_t[t] = (T - t + 1)
Neff_t[t] = (T - t + 1) / g_t[t]
