Delete overlapping pores?

[ShaneFranklinSoil]

I am making voronoi to export for microfluidics. I want the particle size to be around the size of sand grains ~0.5 mm. It seems like to get the voronoi this small it comes along with an overlapping pore error. The error won't go away unless particle size becomes quite large.

Any thoughts here?

[jgostick]

you can try the relaxation argument in the Voronoi generator. If you set this to 2 or 3, the base points will move away from each other so they is room for larger pores. Without this there will always be pores which are quite close together.

[ShaneFranklinSoil]

By macropores I mean the overlapping red

[jgostick]

I was feeling bored today, so spent 30 minutes doing this:

import openpnm as op
import numpy as np

net, vor = op._skgraph.generators.voronoi(
    shape=[1, 1, 0],
    points=100,
    relaxation=5,
    reflect=True,
    node_prefix='pore',
    edge_prefix='throat',
)
# add delaunay points
pn = op.network.Network()
pn.update(net)
pn['pore.voronoi'] = True
pts = np.hstack((vor.points[:100], np.zeros([100, 1])))
op.topotools.extend(pn, pore_coords=pts)
pn.add_model(
    propname='pore.diameter',
    model=op.models.geometry.pore_size.largest_sphere,
    domain='pore.voronoi',
)
pn['pore.delaunay'] = False
pn['pore.delaunay'][pn.pores('voronoi', mode='not')] = True
pn['pore.diameter@delaunay'] = 0.1

# %%
h = op.visualization.plot_connections(
    pn,
    throats=pn.throats('all'),
)
h = op.visualization.plot_coordinates(
    pn,
    pores=pn.pores('voronoi'),
    size_by=pn['pore.diameter']**2,
    s=500,
    ax=h,
)
h = op.visualization.plot_coordinates(
    pn,
    pores=pn.pores('delaunay'),
    size_by=pn['pore.diameter']**2,
    s=500,
    c='g',
    ax=h,
)

Which produces this:

[jgostick]

Also, not sure what your final aim is exactly, but we have added this to PoreSpy:

https://porespy.org/examples/generators/reference/cylindrical_pillars_mesh.html

[ShaneFranklinSoil]

You're a legend! Sorry I am new to coding and open pnm. This is incredible

[jgostick]

The reason the code above is a bit on the verbose and obscure side is because there is a bug in the DelaunayVoronoiDual generator, which I opened an issue for #2913. Otherwise you could have it all with just one line.