max_flow Namespace Reference

Functions
	compute_backbone (ase_atoms, backbone_atoms, flow_atoms, reeb_stride, common_backbone=True, apply_frechet_mean=False, print_mean_stucture=False, repeat=(1, 1, 1), radii_figures=False)
	compute_max_flow (backbone_mean, backbone_radii, M, m, grid_spacing, volume, fat, reeb_stride, stride, periodic, save_rb=False, verbose=False)
	rdf_onset_radius (distances_flat, box_volume, n_bins=200, rrange=6, threshold=0.01, label="", radii_figures=False)
	unwrap_trajectory (atoms, cell)

Function Documentation

compute_backbone()

max_flow.compute_backbone	(		ase_atoms,
			backbone_atoms,
			flow_atoms,
			reeb_stride,
			common_backbone = True,
			apply_frechet_mean = False,
			print_mean_stucture = False,
			repeat = (1, 1, 1),
			radii_figures = False )

Compute backbone radii and flow coordinates

compute_max_flow()

max_flow.compute_max_flow	(		backbone_mean,
			backbone_radii,
			M,
			m,
			grid_spacing,
			volume,
			fat,
			reeb_stride,
			stride,
			periodic,
			save_rb = False,
			verbose = False )

Compute reeb_graph and max flow

rdf_onset_radius()

max_flow.rdf_onset_radius	(		distances_flat,
			box_volume,
			n_bins = 200,
			rrange = 6,
			threshold = 0.01,
			label = "",
			radii_figures = False )

Find the onset of the first peak in the RDF

unwrap_trajectory()

max_flow.unwrap_trajectory	(		atoms,
			cell )