order package

Submodules

order.XYZ module

XYZ trajectory reader

class order.XYZ.XYZLoader(filename)

Bases: object

close()

close XYZ file if it was open

read_all_frames()

read all frames of XYZ trajectory

read_n_frames()

get the starting position of each frame

read_next_frame(frame)

read a frame of XYZ trajectory

order.avc module

class order.avc.VoronoiCell(filename, center, bins=100)

Bases: order.oto.Orientational

asphericity of the Voronoi cell

asphericity(freq=1)

compute asphericity of the Voronoi cell

compute_vc(points)

compute the Voronoi cell

polyhedron(coords, j, L)

find the polyhedron for center molecule

wrap_box(c_coord, coords, L)

wrap the simulation box

order.lsi module

order.order module

order.order.command_line_runner()

order.order.get_parser()

order.oto module

Orientational Tetrahedral Order q

class order.oto.Orientational(trajectory, center, bins=100)

Bases: object

orientational tetrahedral order parameter

four_neighbors(coords, L)

compute four nearest water oxygen neighbors

orientational_param(freq=1)

compute orientational order parameter

out_put(taskname='OTO', param_name='Q')

output raw data and distribution

order.plot module

class order.plot.plot(filename, taskname)

Bases: object

plotting

plot_distribution()

plot distribution

order.tto module

Translational Tetrahedral Order Sk

class order.tto.Translational(filename, center, bins=100)

Bases: order.oto.Orientational

translational tetrahedral order parameter

translational_param(freq=1)

compute translational order parameter

order.util module

order.util.cos_angle(v1, v2)

compute the cos angle of two giving vectors

order.util.output_end(t_start, t_end)

print total running time

order.util.output_system_info(filename, n_atoms, n_frames)

print system information

order.util.output_task(name, freq, bins, center)

print task information

order.util.output_welcome()

print welcome information

order.util.pbc(dx, dy, dz, L)

periodic boundary conditions

Module contents