VolterraBasis API

Loading trajectories

xframe(x, time[, v, a, fix_time, round_time, dt])

Creates a xarray dataset (['t', 'x']) from a trajectory.

compute_va(xf[, correct_jumps, jump, ...])

Computes velocity and acceleration from a dataset with ['t', 'x'] as returned by xframe.

compute_a(xvf)

Computes the acceleration from a dataset with ['t', 'x', 'v'].

concat_underdamped(xva)

Return the DataSet such that x is now (x,v) and v is now (v,a),

compute_1d_fe(xva_list[, bins, kT, hist])

Computes the free energy from the trajectoy using a cubic spline interpolation.

Memory kernel estimation

Estimator_gle(xva_arg, model_class, basis[, ...])

The main class for the position dependent memory extraction holding all data.

Available models of GLE

Pos_gle(*args, **kwargs)

The main class for the position dependent memory extraction, holding all data and the extracted memory kernels.

Pos_gle_with_friction(*args, **kwargs)

A derived class in which we don't enforce zero instantaneous friction

Pos_gle_no_vel_basis(*args, **kwargs)

Use basis function dependent of the position only

Pos_gle_const_kernel(*args, **kwargs)

A derived class in which we the kernel is computed independent of the position

Pos_gle_overdamped(*args[, L_obs, ...])

Extraction of position dependent memory kernel for overdamped dynamics.

Pos_gle_hybrid(*args, **kwargs)

Implement the hybrid projector of arXiv:2202.01922

Basis Features

VolterraBasis.basis.LinearFeatures([to_center])

Linear function

VolterraBasis.basis.PolynomialFeatures([...])

Wrapper for numpy polynomial series.

VolterraBasis.basis.FourierFeatures([order, ...])

Fourier series.

VolterraBasis.basis.BSplineFeatures([...])

Bsplines features class

VolterraBasis.basis.FEMScalarFeatures(basis)

Finite elements features for scalar basis

VolterraBasis.basis.SmoothIndicatorFeatures(...)

Indicator function with smooth boundary

VolterraBasis.basis.SplineFctFeatures(knots, ...)

A single basis function that is given from splines fit of data

VolterraBasis.basis.FeaturesCombiner(*basis)

Allow to combine features to build composite basis

VolterraBasis.basis.TensorialBasis2D(b1[, b2])

Combine two 1D basis to get a 2D basis