How to use the openpnm.geometry.StickAndBall function in openpnm

The diffusing species diffuses through air, which is followed by mass
    partitioning at the two air-water interfaces, then continues diffusing
    through the water, and finally reacting at the two reacting plates at the
    top and the bottom of the network.

"""
import openpnm as op
import numpy as np
import matplotlib.pyplot as plt
np.random.seed(10)


# Define network, geometry and constituent phases
net = op.network.Cubic(shape=[100, 100, 1])
geom = op.geometry.StickAndBall(network=net)
air = op.phases.Air(network=net, name="air")
water = op.phases.Water(network=net, name="water")
water["pore.diffusivity"] = air["pore.diffusivity"] * 0.05

# Define the regions to be occupied by the two phases (air and water)
x, y, z = net["pore.coords"].T
ps_water = net.Ps[(y >= 75) + (y <= 25)]
ps_air = np.setdiff1d(net.Ps, ps_water)
ts_water = net.find_neighbor_throats(pores=ps_water, mode="xnor")
ts_air = net.find_neighbor_throats(pores=ps_air, mode="xnor")
ts_interface = net.find_neighbor_throats(pores=ps_water, mode="xor")

# Define multiphase and set phase occupancy
mphase = op.phases.MultiPhase(network=net, phases=[air, water], name="mphase")
mphase._set_automatic_throat_occupancy()
mphase.set_occupancy(air, pores=ps_air, throats=ts_air)

import pytest
import openpnm as op
ws = op.Workspace()
proj = ws.new_project()

pn = op.network.Cubic(shape=[10, 10, 10], spacing=1e-4, project=proj)
Ps = pn['pore.coords'][:, 0] < pn['pore.coords'][:, 0].mean()
Ts = pn.find_neighbor_throats(pores=Ps, mode='xnor')
geo1 = op.geometry.StickAndBall(network=pn, pores=Ps, throats=Ts)

Ps = pn['pore.coords'][:, 0] >= pn['pore.coords'][:, 0].mean()
Ts = pn.find_neighbor_throats(pores=Ps, mode='or')
geo2 = op.geometry.StickAndBall(network=pn, pores=Ps, throats=Ts)

pn['pore.foo'] = 1
# Can't create a subdict below foo
with pytest.raises(Exception):
    pn['pore.foo.bar'] = 1
# Can create a subdict directly
pn['pore.baz.bar'] = 2
# Can't create a new item already used as subdict
with pytest.raises(Exception):
    pn['pore.baz'] = 2

# Also works on subdomains
geo1['pore.blah'] = 1
with pytest.raises(Exception):
    geo1['pore.blah.boo'] = 1
geo1['pore.bee.bop'] = 1

import openpnm as op
ws = op.Workspace()
proj = ws.new_project()

pn = op.network.Cubic(shape=[10, 10, 10], spacing=1e-4, project=proj)
geo = op.geometry.StickAndBall(network=pn, pores=pn.Ps, throats=pn.Ts)
air = op.phases.Air(network=pn, name='air')
water = op.phases.Water(network=pn, name='h2o')
hg = op.phases.Mercury(network=pn, name='hg')
phys_air = op.physics.Standard(network=pn, phase=air, geometry=geo)
phys_water = op.physics.Standard(network=pn, phase=water, geometry=geo)
phys_hg = op.physics.Standard(network=pn, phase=hg, geometry=geo)

mip = op.algorithms.Porosimetry(network=pn)
mip.setup(phase=hg)
mip.set_inlets(pores=pn.pores(['top', 'bottom']))
mip.run()
hg.update(mip.results(Pc=70000))
# mip.plot_intrusion_curve()

perm = op.algorithms.StokesFlow(network=pn)
perm.setup(phase=water)

import openpnm as op
import scipy as sp
import matplotlib.pyplot as plt

ws = op.core.Workspace()
ws.settings['local_data'] = True

# NETWORK
sp.random.seed(17)
nx, ny, nz = 80, 160, 1
pn = op.network.Cubic(shape=[nx, ny, nz], spacing=1e-4, name='pn11')

# GEOMETRIES
geom = op.geometry.StickAndBall(network=pn, pores=pn.Ps, throats=pn.Ts)

# PHASES
water = op.phases.Water(network=pn)

# PHYSICS
phys_water = op.physics.GenericPhysics(network=pn, phase=water, geometry=geom)

water['throat.viscosity'] = water['pore.viscosity'][0]
mod = op.models.physics.hydraulic_conductance.hagen_poiseuille
phys_water.add_model(propname='throat.hydraulic_conductance',
                     model=mod, viscosity='throat.viscosity')

geom['pore.area'] = sp.pi*(geom['pore.diameter']**2)/4.0
mod2 = op.models.physics.diffusive_conductance.bulk_diffusion
phys_water.add_model(propname='throat.diffusive_conductance',
                     model=mod2, diffusivity='pore.diffusivity')