amep.utils

Utility Methods

The AMEP module amep.utils is a collection of various utility methods.

Functions

average_func(func, data[, skip, nr, indices])	Compute the average of a certain function.
compute_parallel(func, chunks, *args[, ...])	Calls the given function for all given chunks in parallel with a given number of parallel jobs.
detect2peaks(xdata, ydata[, nav, distance, ...])	Detects the two highest peaks in the given data after smoothing it with a running average.
dimension(coords[, verbose])	Returns the spatial dimension of simulation data.
domain_length(s_fac, q[, qmin, qmax])	Calculate the domain length from the structure factor.
envelope(f[, x])	Calculates the envelope of the data f by determining all local peaks of the data.
group_jobs(joblist, nworkers)	Groups the given jobs into groups of length nworkers.
in_box(coords, box_boundary[, values, ...])	Returns all coordinates in coords that are in the given simulation box boundaries (including the boundary).
in_circle(coords, radius[, center, values, ...])	Returns the coordinates/values for only particles inside or outside a circular/spherical region of a given radius and centered around a given center position.
kpeaks(Sxy, kx, ky[, a, dk, mode])	Calculates the wave vectors that correspond to the first peaks of the 2D structure factor.
log_indices(first, last[, num])	Creates logarithmically spaced indices.
mesh_to_coords(X, Y)	Converts positions in two-dimensional space given as a meshgrid into an array of two-dimensional position vectors of shape (N,2), where N is the total number of positions in the given meshgrid.
msd_from_vacf(vacf, times)	Calculates the mean square displacement from the integral of the velocity autocorrelation function.
optimal_chunksize(data_length, ...[, ...])	Estimates an optimal chunksize for limiting the RAM usage.
profile(coords, box_boundary, values[, ...])	Calculate the profile of given values.
rfft(data[, delta])	Real fast Fourier transform.
rotate_coords(coords, theta, center)	Rotates all coordinate vectors given in coords by the angle theta around the origin of the system given by center.
rotation(theta[, axis])	Rotation matrix in 3D for rotation around a certain axis.
runningmean(data, nav[, mode])	Compute the running mean of a 1-dimensional array.
runningmean2d(data, nav[, mode])	Computes the running mean of two-dimensional data, e.g., of a 2d density field.
segmented_mean(data, n[, verbose])	Compute the mean of n adjacent data points.
segmented_mean2d(data, n[, verbose])	Compute the mean of n*n adjacent data points.
spectrum(xdata, ydata)	Calculates the spectrum of one-dimensional real data by using fft.
sq_from_gr(r, gr, q, rho[, twod])	Compute the static structure factor as fourier transform of the pair correlation function.
sq_from_sf2d(S, Qx, Qy)	Calculates the isotropic static structure factor from the two-dimensional static structure factor by making a spherical average/radial mean.
traj_slice(N, skip, nr_averages)	Slicing object to slice a trajectory.
unit_vector_2D(theta)	Generates 2D unit vectors in the x-y plane with angle theta to the x axis.
unit_vector_3D(theta, phi)	Generates 3D unit vectors with components
upper_triangle(matrix[, diagonal, indices])	Returns the upper diagonal of a quadratic matrix.
weighted_runningmean(data, nav[, kernel, ...])	Compute the weighted running mean of a 1-dimensional array.
weighted_runningmean2d(data, nav[, kernel, ...])	Compute the running mean of two-dimensional data.