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[thermo] making docstring for estimate_umbrella_sampling() explicit o…
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…n how to pass trajecttories, us_centers, and us_force_constants
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cwehmeyer committed Jun 13, 2016
1 parent 5f61546 commit 8da1247
Showing 1 changed file with 5 additions and 2 deletions.
7 changes: 5 additions & 2 deletions pyemma/thermo/api.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,10 +57,10 @@ def estimate_umbrella_sampling(
us_dtrajs : list of N int arrays, each of shape (T_i,)
The integers are indexes in 0,...,n-1 enumerating the n discrete states or the bins the
umbrella sampling trajectory is in at any time.
us_centers : array-like of size N
us_centers : list of N floats or d-dimensional arrays of floats
List or array of N center positions. Each position must be a d-dimensional vector. For 1d
umbrella sampling, one can simply pass a list of centers, e.g. [-5.0, -4.0, -3.0, ... ].
us_force_constants : float or array-like of float
us_force_constants : list of N floats or d- or dxd-dimensional arrays of floats
The force constants used in the umbrellas, unit-less (e.g. kT per squared length unit). For
multidimensional umbrella sampling, the force matrix must be used.
md_trajs : list of M arrays, each of shape (T_i, d), optional, default=None
Expand Down Expand Up @@ -148,6 +148,9 @@ def estimate_umbrella_sampling(
from .util import get_umbrella_sampling_data as _get_umbrella_sampling_data
ttrajs, btrajs, umbrella_centers, force_constants, unbiased_state = _get_umbrella_sampling_data(
us_trajs, us_centers, us_force_constants, md_trajs=md_trajs, kT=kT)
for traj, dtraj in zip(us_trajs, us_dtrajs):
if traj.shape[0] != dtraj.shape[0]:
raise ValueError("unmatching trajectory lengths")
if md_dtrajs is None:
md_dtrajs = []
estimator_obj = None
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