mdgo.residence_time module

This module calculates species correlation lifetime (residence time).

mdgo.residence_time.neighbors_one_atom(nvt_run, center_atom, species, select_dict, distance, run_start, run_end)

Create adjacency matrix for one center atom.

Parameters

• nvt_run (Universe) – An MDAnalysis Universe.

• center_atom (Atom) – The center atom object.

• species (str) – The neighbor species in the select_dict.

• select_dict (Dict[str, str]) – A dictionary of atom species selection, where each atom species name is a key and the corresponding values are the selection language.

• distance (float) – The neighbor cutoff distance.

• run_start (int) – Start frame of analysis.

• run_end (int) – End frame of analysis.

Return type

Dict[str, ndarray]

Returns

A neighbor dict with neighbor atom id as keys and arrays of adjacent boolean (0/1) as values.

mdgo.residence_time.calc_acf(a_values)

Calculate auto-correlation function (ACF)

Parameters

• a_values (Dict[str, ndarray]) – A dict of adjacency matrix with neighbor atom id as keys and arrays

• boolean (of adjacent) –

Return type

List[ndarray]

Returns

A list of auto-correlation functions for each neighbor species.

mdgo.residence_time.exponential_func(x, a, b, c)

An exponential decay function

Parameters

• x (Union[float, floating, ndarray]) – Independent variable.

• a (Union[float, floating, ndarray]) – Initial quantity.

• b (Union[float, floating, ndarray]) – Exponential decay constant.

• c (Union[float, floating, ndarray]) – Constant.

Return type

Union[floating, ndarray]

Returns

The acf

mdgo.residence_time.calc_neigh_corr(nvt_run, distance_dict, select_dict, time_step, run_start, run_end, center_atom='cation')

Calculates the neighbor auto-correlation function (ACF) of selected species around center atom.

Parameters

• nvt_run (Universe) – An MDAnalysis Universe.

• distance_dict (Dict[str, float]) –

• select_dict (Dict[str, str]) –

• time_step (float) –

• run_start (int) – Start frame of analysis.

• run_end (int) – End frame of analysis.

• center_atom (str) – The center atom to calculate the ACF for. Default to “cation”.

Return type

Tuple[ndarray, Dict[str, ndarray]]

Returns

A tuple containing the time series, and a dict of acf of neighbor species.

mdgo.residence_time.fit_residence_time(times, acf_avg_dict, cutoff_time, time_step)

Use the ACF to fit the residence time (Exponential decay constant). TODO: allow defining the residence time according to a threshold value of the decay

Parameters

• times (ndarray) – A time series.

• acf_avg_dict (Dict[str, ndarray]) – A dict containing the ACFs of the species.

• cutoff_time (int) – Fitting cutoff time.

• time_step (float) – The time step between each frame, in ps.

Return type

Dict[str, floating]

Returns

A dict containing residence time of each species