def run(self, phase=None, throats=None):
logger.warning('This algorithm can take some time...')
conduit_lengths = sp.sum(misc.conduit_lengths(network=self._net,
mode='centroid'), axis=1)
graph = self._net.create_adjacency_matrix(data=conduit_lengths,
sprsfmt='csr')
if phase is not None:
self._phase = phase
if 'throat.occupancy' in self._phase.props():
temp = conduit_lengths*(self._phase['throat.occupancy'] == 1)
graph = self._net.create_adjacency_matrix(data=temp,
sprsfmt='csr',
prop='temp')
path = spgr.shortest_path(csgraph=graph, method='D', directed=False)
Px = sp.array(self._net['pore.coords'][:, 0], ndmin=2)
Py = sp.array(self._net['pore.coords'][:, 1], ndmin=2)
Pz = sp.array(self._net['pore.coords'][:, 2], ndmin=2)
Cx = sp.square(Px.T - Px)
Cy = sp.square(Py.T - Py)
Cz = sp.square(Pz.T - Pz)
Ds = sp.sqrt(Cx + Cy + Cz)
temp = path / Ds
temp[sp.isnan(temp)] = 0
temp[sp.isinf(temp)] = 0
return temp
def run(self, phase=None, throats=None):
logger.warning('This algorithm can take some time...')
conduit_lengths = sp.sum(misc.conduit_lengths(network=self._net,
mode='centroid'), axis=1)
graph = self._net.create_adjacency_matrix(data=conduit_lengths,
sprsfmt='csr')
if phase is not None:
self._phase = phase
if 'throat.occupancy' in self._phase.props():
temp = conduit_lengths*(self._phase['throat.occupancy'] == 1)
graph = self._net.create_adjacency_matrix(data=temp,
sprsfmt='csr',
prop='temp')
path = spgr.shortest_path(csgraph=graph, method='D', directed=False)
Px = sp.array(self._net['pore.coords'][:, 0], ndmin=2)
Py = sp.array(self._net['pore.coords'][:, 1], ndmin=2)
Pz = sp.array(self._net['pore.coords'][:, 2], ndmin=2)
Cx = sp.square(Px.T - Px)
Cy = sp.square(Py.T - Py)
Cz = sp.square(Pz.T - Pz)
Ds = sp.sqrt(Cx + Cy + Cz)
temp = path / Ds
temp[sp.isnan(temp)] = 0
temp[sp.isinf(temp)] = 0
return temp
def bulk_diffusion(physics,
phase,
network,
pore_molar_density='pore.molar_density',
pore_diffusivity='pore.diffusivity',
pore_area='pore.area',
pore_diameter='pore.diameter',
throat_area='throat.area',
throat_length='throat.length',
throat_diameter='throat.diameter',
shape_factor='throat.shape_factor',
calc_pore_len=False,
**kwargs):
r"""
Calculate the diffusive conductance of conduits in network, where a
conduit is ( 1/2 pore - full throat - 1/2 pore ) based on the areas
Parameters
----------
network : OpenPNM Network Object
phase : OpenPNM Phase Object
The phase of interest
Notes
-----
(1) This function requires that all the necessary phase properties already
be calculated.
(2) This function calculates the specified property for the *entire*
network then extracts the values for the appropriate throats at the end.
"""
# Get Nt-by-2 list of pores connected to each throat
Ps = network['throat.conns']
# Get properties in every pore in the network
parea = network[pore_area]
pdia = network[pore_diameter]
# Get the properties of every throat
tdia = network[throat_diameter]
tarea = _sp.pi * (tdia / 2)**2
tlen = network[throat_length]
# Interpolate pore phase property values to throats
cp = phase[pore_molar_density]
ct = phase.interpolate_data(data=cp)
DABp = phase[pore_diffusivity]
DABt = phase.interpolate_data(data=DABp)
if calc_pore_len:
lengths = misc.conduit_lengths(network, mode='centroid')
plen1 = lengths[:, 0]
plen2 = lengths[:, 2]
else:
plen1 = (0.5 * pdia[Ps[:, 0]])
plen2 = (0.5 * pdia[Ps[:, 1]])
# Remove any non-positive lengths
plen1[plen1 <= 0] = 1e-12
plen2[plen2 <= 0] = 1e-12
# Find g for half of pore 1
gp1 = ct * DABt * parea[Ps[:, 0]] / plen1
gp1[_sp.isnan(gp1)] = _sp.inf
gp1[~(gp1 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for half of pore 2
gp2 = ct * DABt * parea[Ps[:, 1]] / plen2
gp2[_sp.isnan(gp2)] = _sp.inf
gp2[~(gp2 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for full throat, remove any non-positive lengths
tlen[tlen <= 0] = 1e-12
# Get shape factor
try:
sf = network[shape_factor]
except:
sf = _sp.ones(network.num_throats())
sf[_sp.isnan(sf)] = 1.0
gt = (1 / sf) * ct * DABt * tarea / tlen
# Set 0 conductance pores (boundaries) to inf
gt[~(gt > 0)] = _sp.inf
value = (1 / gt + 1 / gp1 + 1 / gp2)**(-1)
value = value[phase.throats(physics.name)]
return value
def hagen_poiseuille(physics, phase, network, pore_diameter='pore.diameter',
pore_viscosity='pore.viscosity', throat_length='throat.length',
throat_diameter='throat.diameter', calc_pore_len=True,
shape_factor='throat.shape_factor',
**kwargs):
r"""
Calculates the hydraulic conductivity of throat assuming cylindrical
geometry using the Hagen-Poiseuille model
Parameters
----------
network : OpenPNM Network Object
phase : OpenPNM Phase Object
Notes
-----
(1) This function requires that all the necessary phase properties already
be calculated.
(2) This function calculates the specified property for the *entire*
network then extracts the values for the appropriate throats at the end.
"""
# Get Nt-by-2 list of pores connected to each throat
Ps = network['throat.conns']
# Get properties in every pore in the network
mup = phase[pore_viscosity]
mut = phase.interpolate_data(mup)
pdia = network[pore_diameter]
if calc_pore_len:
lengths = misc.conduit_lengths(network, mode='centroid')
plen1 = lengths[:, 0]
plen2 = lengths[:, 2]
else:
plen1 = (0.5*pdia[Ps[:, 0]])
plen2 = (0.5*pdia[Ps[:, 1]])
# Remove any non-positive lengths
plen1[plen1 <= 0] = 1e-12
plen2[plen2 <= 0] = 1e-12
# Find g for half of pore 1
gp1 = _sp.pi*(pdia[Ps[:, 0]])**4/(128*plen1*mut)
gp1[_sp.isnan(gp1)] = _sp.inf
gp1[~(gp1 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for half of pore 2
gp2 = _sp.pi*(pdia[Ps[:, 1]])**4/(128*plen2*mut)
gp2[_sp.isnan(gp2)] = _sp.inf
gp2[~(gp2 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for full throat
tdia = network[throat_diameter]
tlen = network[throat_length]
# Remove any non-positive lengths
tlen[tlen <= 0] = 1e-12
# Get shape factor
try:
sf = network[shape_factor]
except:
sf = _sp.ones(network.num_throats())
sf[_sp.isnan(sf)] = 1.0
gt = (1/sf)*_sp.pi*(tdia)**4/(128*tlen*mut)
gt[~(gt > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
value = (1/gt + 1/gp1 + 1/gp2)**(-1)
value = value[phase.throats(physics.name)]
return value
def bulk_diffusion(physics, phase, network, pore_molar_density='pore.molar_density',
pore_diffusivity='pore.diffusivity', pore_area='pore.area',
pore_diameter='pore.diameter', throat_area='throat.area',
throat_length='throat.length', throat_diameter='throat.diameter',
calc_pore_len=True, shape_factor='throat.shape_factor', **kwargs):
r"""
Calculate the diffusive conductance of conduits in network, where a
conduit is ( 1/2 pore - full throat - 1/2 pore ) based on the areas
Parameters
----------
network : OpenPNM Network Object
phase : OpenPNM Phase Object
The phase of interest
Notes
-----
(1) This function requires that all the necessary phase properties already
be calculated.
(2) This function calculates the specified property for the *entire*
network then extracts the values for the appropriate throats at the end.
"""
# Get Nt-by-2 list of pores connected to each throat
Ps = network['throat.conns']
# Get properties in every pore in the network
parea = network[pore_area]
pdia = network[pore_diameter]
# Get the properties of every throat
tdia = network[throat_diameter]
tarea = _sp.pi*(tdia/2)**2
tlen = network[throat_length]
# Interpolate pore phase property values to throats
cp = phase[pore_molar_density]
ct = phase.interpolate_data(data=cp)
DABp = phase[pore_diffusivity]
DABt = phase.interpolate_data(data=DABp)
if calc_pore_len:
lengths = misc.conduit_lengths(network, mode='centroid')
plen1 = lengths[:, 0]
plen2 = lengths[:, 2]
else:
plen1 = (0.5*pdia[Ps[:, 0]])
plen2 = (0.5*pdia[Ps[:, 1]])
# Remove any non-positive lengths
plen1[plen1 <= 0] = 1e-12
plen2[plen2 <= 0] = 1e-12
# Find g for half of pore 1
gp1 = ct*DABt*parea[Ps[:, 0]] / plen1
gp1[_sp.isnan(gp1)] = _sp.inf
gp1[~(gp1 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for half of pore 2
gp2 = ct*DABt*parea[Ps[:, 1]] / plen2
gp2[_sp.isnan(gp2)] = _sp.inf
gp2[~(gp2 > 0)] = _sp.inf # Set 0 conductance pores (boundaries) to inf
# Find g for full throat, remove any non-positive lengths
tlen[tlen <= 0] = 1e-12
# Get shape factor
try:
sf = network[shape_factor]
except:
sf = _sp.ones(network.num_throats())
sf[_sp.isnan(sf)] = 1.0
gt = (1/sf)*ct*DABt*tarea/tlen
# Set 0 conductance pores (boundaries) to inf
gt[~(gt > 0)] = _sp.inf
value = (1/gt + 1/gp1 + 1/gp2)**(-1)
value = value[phase.throats(physics.name)]
return value
