def test_ionic_conductance_electroneutrality(self):
sw = mixtures.SalineWater(network=self.net)
Na = sw.components[f'Na_{sw.name}']
Cl = sw.components[f'Cl_{sw.name}']
self.phys = op.physics.GenericPhysics(network=self.net, phase=sw, geometry=self.geo)
sw[f'pore.concentration.{Cl.name}'] = np.linspace(10, 20, 27) * 0.5
sw[f'pore.concentration.{Na.name}'] = np.linspace(10, 20, 27)
electroneutrality = op.models.physics.ionic_conductance.electroneutrality
self.phys.add_model(propname='throat.ionic_conductance',
model=electroneutrality, ions=[Na.name, Cl.name])
self.phys.regenerate_models()
actual = np.mean(self.phys['throat.ionic_conductance'])
assert_allclose(actual, desired=0.0116345, rtol=1e-5)
def setup_class(self):
# network
np.random.seed(0)
self.net = op.network.Cubic(shape=[6, 6, 1], spacing=1e-6)
prs = (self.net['pore.back'] * self.net['pore.right'] +
self.net['pore.back'] * self.net['pore.left'] +
self.net['pore.front'] * self.net['pore.right'] +
self.net['pore.front'] * self.net['pore.left'])
prs = self.net.Ps[prs]
thrts = self.net['throat.surface']
thrts = self.net.Ts[thrts]
op.topotools.trim(network=self.net, pores=prs, throats=thrts)
np.random.seed(0)
op.topotools.reduce_coordination(self.net, 3)
# geometry
np.random.seed(0)
self.geo = op.geometry.StickAndBall(network=self.net,
pores=self.net.Ps,
throats=self.net.Ts)
# phase
self.sw = mixtures.SalineWater(network=self.net)
# Retrieve handles to each species for use below
self.Na = self.sw.components['Na_' + self.sw.name]
self.Cl = self.sw.components['Cl_' + self.sw.name]
self.H2O = self.sw.components['H2O_' + self.sw.name]
# physics
self.phys = op.physics.GenericPhysics(network=self.net,
phase=self.sw,
geometry=self.geo)
modphys = op.models.physics
self.flow = modphys.hydraulic_conductance.hagen_poiseuille
self.phys.add_model(propname='throat.hydraulic_conductance',
pore_viscosity='pore.viscosity',
throat_viscosity='throat.viscosity',
model=self.flow,
regen_mode='normal')
self.current = modphys.ionic_conductance.electroneutrality
self.phys.add_model(propname='throat.ionic_conductance',
ions=[self.Na.name, self.Cl.name],
model=self.current,
regen_mode='normal')
self.eA_dif = modphys.diffusive_conductance.ordinary_diffusion
self.phys.add_model(
propname=('throat.diffusive_conductance.' + self.Na.name),
pore_diffusivity=('pore.diffusivity.' + self.Na.name),
throat_diffusivity=('throat.diffusivity.' + self.Na.name),
model=self.eA_dif,
regen_mode='normal')
self.eB_dif = modphys.diffusive_conductance.ordinary_diffusion
self.phys.add_model(
propname=('throat.diffusive_conductance.' + self.Cl.name),
pore_diffusivity=('pore.diffusivity.' + self.Cl.name),
throat_diffusivity=('throat.diffusivity.' + self.Cl.name),
model=self.eB_dif,
regen_mode='normal')
scheme = 'powerlaw'
self.ad_dif_mig_Na = modphys.ad_dif_mig_conductance.ad_dif_mig
self.phys.add_model(propname=('throat.ad_dif_mig_conductance.' +
self.Na.name),
pore_pressure='pore.pressure',
model=self.ad_dif_mig_Na,
ion=self.Na.name,
s_scheme=scheme)
self.ad_dif_mig_Cl = modphys.ad_dif_mig_conductance.ad_dif_mig
self.phys.add_model(propname=('throat.ad_dif_mig_conductance.' +
self.Cl.name),
pore_pressure='pore.pressure',
model=self.ad_dif_mig_Cl,
ion=self.Cl.name,
s_scheme=scheme)
# settings for algorithms
setts1 = {
'solver_max_iter': 5,
'solver_tol': 1e-08,
'solver_rtol': 1e-08,
'nlin_max_iter': 10,
'cache_A': False,
'cache_b': False
}
setts2 = {
'g_tol': 1e-4,
'g_max_iter': 100,
't_output': 1000,
't_step': 500,
't_final': 20000,
't_scheme': 'implicit'
}
# algorithms
self.sf = op.algorithms.StokesFlow(network=self.net,
phase=self.sw,
settings=setts1)
self.sf.set_value_BC(pores=self.net.pores('right'), values=11)
self.sf.set_value_BC(pores=self.net.pores('left'), values=10)
self.p = op.algorithms.TransientIonicConduction(network=self.net,
phase=self.sw,
settings=setts1)
self.p.set_value_BC(pores=self.net.pores('back'), values=0.02)
self.p.set_value_BC(pores=self.net.pores('front'), values=0.01)
self.p.settings['charge_conservation'] = 'laplace'
self.eA = op.algorithms.TransientNernstPlanck(network=self.net,
phase=self.sw,
ion=self.Na.name,
settings=setts1)
self.eA.set_value_BC(pores=self.net.pores('right'), values=20)
self.eA.set_value_BC(pores=self.net.pores('left'), values=10)
self.eB = op.algorithms.TransientNernstPlanck(network=self.net,
phase=self.sw,
ion=self.Cl.name,
settings=setts1)
self.eB.set_value_BC(pores=self.net.pores('right'), values=20)
self.eB.set_value_BC(pores=self.net.pores('left'), values=10)
mnp = op.algorithms.TransientNernstPlanckMultiphysicsSolver
self.mnp = mnp(network=self.net, phase=self.sw, settings=setts2)
self.mnp.setup(potential_field=self.p.name,
ions=[self.eA.name, self.eB.name])
prs = net.Ps[prs]
thrts = net['throat.surface']
thrts = net.Ts[thrts]
op.topotools.trim(network=net, pores=prs, throats=thrts)
np.random.seed(0)
op.topotools.reduce_coordination(net, 3)
np.random.seed(0)
geo = op.geometry.CirclesAndRectangles(network=net,
pores=net.Ps,
throats=net.Ts)
sw = mixtures.SalineWater(network=net)
# Retrieve handles to each species for use below
Na = sw.components['Na_' + sw.name]
Cl = sw.components['Cl_' + sw.name]
H2O = sw.components['H2O_' + sw.name]
# Create physics
phys = op.physics.GenericPhysics(network=net, phase=sw, geometry=geo)
flow = op.models.physics.hydraulic_conductance.hagen_poiseuille
phys.add_model(propname='throat.hydraulic_conductance',
pore_viscosity='pore.viscosity',
throat_viscosity='throat.viscosity',
model=flow,
regen_mode='normal')
def setup_class(self):
np.random.seed(0)
self.net = op.network.Cubic(shape=[8, 8, 1], spacing=9e-4)
prs = (self.net["pore.back"] * self.net["pore.right"] +
self.net["pore.back"] * self.net["pore.left"] +
self.net["pore.front"] * self.net["pore.right"] +
self.net["pore.front"] * self.net["pore.left"])
thrts = self.net["throat.surface"]
op.topotools.trim(network=self.net,
pores=self.net.Ps[prs],
throats=self.net.Ts[thrts])
self.geo = op.geometry.StickAndBall(network=self.net,
pores=self.net.Ps,
throats=self.net.Ts)
pr_d = op.models.misc.constant
trt_d = op.models.misc.constant
self.geo.add_model(propname="pore.diameter", model=pr_d, value=1.5e-4)
self.geo.add_model(propname="throat.diameter", model=trt_d, value=1e-4)
self.geo.regenerate_models()
self.phase = mixtures.SalineWater(network=self.net)
# Retrieve handles to each species for use below
self.Na = self.phase.components['Na_' + self.phase.name]
self.Cl = self.phase.components['Cl_' + self.phase.name]
self.H2O = self.phase.components['H2O_' + self.phase.name]
# physics
self.phys = op.physics.GenericPhysics(network=self.net,
phase=self.phase,
geometry=self.geo)
flow = op.models.physics.hydraulic_conductance.hagen_poiseuille
self.phys.add_model(
propname="throat.hydraulic_conductance",
pore_viscosity="pore.viscosity",
throat_viscosity="throat.viscosity",
model=flow,
regen_mode="normal",
)
current = op.models.physics.ionic_conductance.electroneutrality
self.phys.add_model(
propname="throat.ionic_conductance",
ions=[self.Na.name, self.Cl.name],
model=current,
regen_mode="normal",
)
eA_dif = op.models.physics.diffusive_conductance.ordinary_diffusion
self.phys.add_model(
propname="throat.diffusive_conductance." + self.Na.name,
pore_diffusivity="pore.diffusivity." + self.Na.name,
throat_diffusivity="throat.diffusivity." + self.Na.name,
model=eA_dif,
regen_mode="normal",
)
eB_dif = op.models.physics.diffusive_conductance.ordinary_diffusion
self.phys.add_model(
propname="throat.diffusive_conductance." + self.Cl.name,
pore_diffusivity="pore.diffusivity." + self.Cl.name,
throat_diffusivity="throat.diffusivity." + self.Cl.name,
model=eB_dif,
regen_mode="normal",
)
# settings for algorithms
self.settings1 = {
"solver_maxiter": 5,
"solver_tol": 1e-08,
"solver_rtol": 1e-08,
"max_iter": 10,
}
self.settings2 = {
"g_tol": 1e-4,
"g_max_iter": 4,
"t_output": 5000,
"t_step": 500,
"t_final": 20000,
"t_scheme": "implicit",
}
def test_init(self):
self.sw = mixtures.SalineWater(network=self.net)
assert isinstance(self.sw, mixtures.GenericMixture)