surface_alg module

Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>

This module is used to mainly to calculate curvatures of a point set surface Such surfaces can be obtained from densities using functions form the density_alg module

CalculateSurface(eh, sampling)

This function estimates the surface of a point set surface by simply summing up the number of points times the infinitesimal surface given by sampling**2.0

CalculateSurface2(eh, within_size=5, PBC=False, cell_center=None, cell_size=None, float_prop_key=None)

This function estimates the surface of a point set surface by simply summing up the number of points times the infinitesimal surface given by sampling**2.0

CalculateNormals(eh, within_size=5, PBC=False, cell_center=False, cell_size=False)

This function assigns normals to each atom in eh No specific orientation of the normals will come out

CalculateNormalsFast2(eh, within_size=5, PBC=False, cell_center=False, cell_size=False)

This function assigns normals to each atom in eh No specific orientation of the normals will come out

CalculateNormalsFast(eh, within_size=15, within_size2=7, PBC=False, cell_center=False, cell_size=False)

This function assigns normals to each atom in eh No specific orientation of the normals will come out

OrientNormalsAlongDensity(eh, density)

OrientNormalsFast(eh, within_size=15, PBC=False, cell_center=None, cell_size=None)

OrientNormals(eh, starting_point, within_size=10, PBC=False, cell_center=None, cell_size=None)

CleanMaxDensitySurface(eh, den_map, n_steps=2, step_size=1, PBC=False, cell_center=None, cell_size=None)

We keep only points that are at a maximum of the density in the direction of the normal

CleanMaxDensitySurface2(eh, den_map, clean_length=10, step_size=1, r=0.7, PBC=False, cell_center=None, cell_size=None)

We keep only points that have a larger density than the other points along the normal

CalculateCurvature(eh, within_size=5, normal_corr=False, PBC=False, cell_center=None, cell_size=None)

This function calculates the principal curvatures k1 and k2 and their direction (principal directions e1 and e2), as well as the gaussian and mean curvature for each atom in the entity and assigns them as FloatProp. Each atom should have a normal vector assigned to it beforehand, as done by the CalculateNormals function.