alchemlyb.preprocessing.subsampling.rst

Subsampling

alchemlyb.preprocessing.subsampling

The functions featured in this module can be used to easily subsample either dHdl <dHdl> or u_nk <u_nk> datasets to give less correlated timeseries.

High-level functions

Two high-level functions ~alchemlyb.preprocessing.subsampling.decorrelate_u_nk and ~alchemlyb.preprocessing.subsampling.decorrelate_dhdl can be used to preprocess the dHdl <dHdl> or u_nk <u_nk> in an automatic fashion. The following code removes an initial "burnin" period and decorrelates the data. :

>>> from alchemlyb.parsing.gmx import extract_u_nk, extract_dHdl
>>> from alchemlyb.preprocessing.subsampling import (decorrelate_u_nk,
>>>     decorrelate_dhdl)
>>> bz = load_benzene().data
>>> u_nk = extract_u_nk(bz['Coulomb'], T=300)
>>> decorrelated_u_nk = decorrelate_u_nk(u_nk, method='dhdl',
>>>     remove_burnin=True)
>>> dhdl = extract_dHdl(bz['Coulomb'], T=300)
>>> decorrelated_dhdl = decorrelate_dhdl(dhdl, remove_burnin=True)

Low-level functions

To decorrelate the data, in addition to the dataframe that contains the dHdl <dHdl> or u_nk <u_nk>, a pandas.Series is needed for the autocorrection analysis. The series could be generated with ~alchemlyb.preprocessing.subsampling.u_nk2series or ~alchemlyb.preprocessing.subsampling.dhdl2series and feed into ~alchemlyb.preprocessing.subsampling.statistical_inefficiency or ~alchemlyb.preprocessing.subsampling.equilibrium_detection. :

>>> from alchemlyb.parsing.gmx import extract_u_nk, extract_dHdl
>>> from alchemlyb.preprocessing.subsampling import (u_nk2series,
>>>     dhdl2series, statistical_inefficiency, equilibrium_detection)
>>> bz = load_benzene().data
>>> u_nk = extract_u_nk(bz['Coulomb'], T=300)
>>> u_nk_series = u_nk2series(u_nk, method='dE')
>>> decorrelate_u_nk = statistical_inefficiency(u_nk, series=u_nk_series)
>>> decorrelate_u_nk = equilibrium_detection(u_nk, series=u_nk_series)
>>> dhdl = extract_dHdl(bz['Coulomb'], T=300)
>>> dhdl_series = dhdl2series(dhdl)
>>> decorrelate_dhdl = statistical_inefficiency(dhdl, series=dhdl_series)
>>> decorrelate_dhdl = equilibrium_detection(dhdl, series=dhdl_series)

API Reference

alchemlyb.preprocessing.subsampling.decorrelate_u_nk

alchemlyb.preprocessing.subsampling.decorrelate_dhdl

alchemlyb.preprocessing.subsampling.u_nk2series

alchemlyb.preprocessing.subsampling.dhdl2series

alchemlyb.preprocessing.subsampling.slicing

alchemlyb.preprocessing.subsampling.statistical_inefficiency

alchemlyb.preprocessing.subsampling.equilibrium_detection