def setup(test_functions, trial_functions, w_, w_1,
dx, ds, normal,
dirichlet_bcs, neumann_bcs,
boundary_to_mark,
permittivity,
density, viscosity,
solutes, enable_PF, enable_EC, enable_NS,
surface_tension, dt, interface_thickness,
grav_const, pf_mobility_coeff, pf_mobility,
q_rhs,
use_iterative_solvers,
p_lagrange,
**namespace):
""" Set up problem. """
# Constants
sigma_bar = surface_tension*3./(2*math.sqrt(2))
per_tau = df.Constant(1./dt)
grav = df.Constant((0., -grav_const))
gamma = pf_mobility_coeff
eps = interface_thickness
# Set up the fields
funs_ = df.split(w_["NSPFEC"])
funs_1 = df.split(w_1["NSPFEC"])
field_number = 0
if enable_NS:
v = test_functions["NSPFEC"][field_number]
u_ = funs_[field_number]
u_1 = funs_1[field_number]
field_number += 1
q = test_functions["NSPFEC"][field_number]
p_ = funs_[field_number]
p_1 = funs_1[field_number]
field_number += 1
if p_lagrange:
q0 = test_functions["NSPFEC"][field_number]
p0_ = funs_[field_number]
p0_1 = funs_1[field_number]
field_number += 1
else:
q0 = p0_ = p0_1 = None
else:
v = u_ = u_1 = q = q0 = p0_ = p0_1 = None
if enable_PF:
psi = test_functions["NSPFEC"][field_number]
phi_ = funs_[field_number]
phi_1 = funs_1[field_number]
field_number += 1
h = test_functions["NSPFEC"][field_number]
g_ = funs_[field_number]
g_1 = funs_1[field_number]
field_number += 1
else:
psi = phi_ = phi_1 = h = g_ = g_1 = 1
if enable_EC:
num_solutes = len(test_functions["NSPFEC"])-field_number-1
b = test_functions["NSPFEC"][field_number:(num_solutes+field_number)]
c_ = funs_[field_number:(num_solutes+field_number)]
c_1 = funs_1[field_number:(num_solutes+field_number)]
U = test_functions["NSPFEC"][num_solutes+field_number]
V_ = funs_[num_solutes+field_number]
V_1 = funs_1[num_solutes+field_number]
else:
b = c_ = c_1 = U = V_ = V_1 = rho_e_ = 0
M_ = pf_mobility(phi_, gamma)
nu_ = ramp(phi_, viscosity)
veps_ = ramp(phi_, permittivity)
rho_ = ramp(phi_, density)
dveps = dramp(permittivity)
drho = dramp(density)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K_ = [] # Diffusivity K[species]
beta_ = [] # Conc. jump func. beta[species]
for solute in solutes:
z.append(solute[1])
K_.append(ramp(phi_, [solute[2], solute[3]]))
beta_.append(ramp(phi_, [solute[4], solute[5]]))
dbeta.append(dramp([solute[4], solute[5]]))
if enable_EC:
rho_e_ = sum([c_e*z_e for c_e, z_e in zip(c_, z)]) # Sum of current sol.
rho_e_1 = sum([c_e*z_e for c_e, z_e in zip(c_1, z)]) # Sum of current sol.
solver = dict()
solver["NSPFEC"] = setup_NSPFEC(w_["NSPFEC"], w_1["NSPFEC"],
dirichlet_bcs["NSPFEC"],
neumann_bcs,
boundary_to_mark,
dx, ds, normal,
v, q, q0, psi, h, b, U,
u_, p_, p0_, phi_, g_, c_, V_,
u_1, p_1, p0_1, phi_1, g_1, c_1, V_1,
M_, nu_, veps_, rho_, K_, beta_, rho_e_,
dbeta, dveps, drho,
per_tau, sigma_bar, eps, grav, z,
solutes,
enable_NS, enable_PF, enable_EC,
use_iterative_solvers,
p_lagrange,
q_rhs)
return dict(solvers=solver)
def setup(mesh, test_functions, trial_functions, w_, w_1, ds, dx, normal,
dirichlet_bcs, neumann_bcs, boundary_to_mark, permittivity, density,
viscosity, solutes, enable_PF, enable_EC, enable_NS, surface_tension,
dt, interface_thickness, grav_const, grav_dir, friction_coeff,
pf_mobility, pf_mobility_coeff, use_iterative_solvers,
use_pressure_stabilization, comoving_velocity, p_lagrange, q_rhs,
**namespace):
""" Set up problem. """
# Constant
dim = mesh.geometry().dim()
sigma_bar = surface_tension * 3. / (2 * math.sqrt(2))
per_tau = df.Constant(1. / dt)
grav = df.Constant(tuple(grav_const * np.array(grav_dir[:dim])))
gamma = pf_mobility_coeff
eps = interface_thickness
fric = df.Constant(friction_coeff)
u_comoving = df.Constant(tuple(comoving_velocity[:dim]))
# Navier-Stokes
u_ = p_ = None
u_1 = p_1 = None
p0 = q0 = p0_ = p0_1 = None
if enable_NS:
u, p = trial_functions["NS"][:2]
v, q = test_functions["NS"][:2]
up_ = df.split(w_["NS"])
up_1 = df.split(w_1["NS"])
u_, p_ = up_[:2]
u_1, p_1 = up_1[:2]
if p_lagrange:
p0 = trial_functions["NS"][-1]
q0 = test_functions["NS"][-1]
p0_ = up_[-1]
p0_1 = up_1[-1]
# Phase field
if enable_PF:
phi, g = trial_functions["PF"]
psi, h = test_functions["PF"]
phi_, g_ = df.split(w_["PF"])
phi_1, g_1 = df.split(w_1["PF"])
else:
# Defaults to phase 1 if phase field is disabled
phi_ = phi_1 = 1.
g_ = g_1 = None
# Electrochemistry
if enable_EC:
num_solutes = len(trial_functions["EC"]) - 1
assert (num_solutes == len(solutes))
c = trial_functions["EC"][:num_solutes]
V = trial_functions["EC"][num_solutes]
b = test_functions["EC"][:num_solutes]
U = test_functions["EC"][num_solutes]
cV_ = df.split(w_["EC"])
cV_1 = df.split(w_1["EC"])
c_, V_ = cV_[:num_solutes], cV_[num_solutes]
c_1, V_1 = cV_1[:num_solutes], cV_1[num_solutes]
else:
c_ = V_ = c_1 = V_1 = None
phi_flt_ = unit_interval_filter(phi_)
phi_flt_1 = unit_interval_filter(phi_1)
M_ = pf_mobility(phi_flt_, gamma)
M_1 = pf_mobility(phi_flt_1, gamma)
mu_ = ramp(phi_flt_, viscosity)
rho_ = ramp(phi_flt_, density)
rho_1 = ramp(phi_flt_1, density)
veps_ = ramp(phi_flt_, permittivity)
dveps = dramp(permittivity)
drho = dramp(density)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K_ = [] # Diffusivity K[species]
beta_ = [] # Conc. jump func. beta[species]
for solute in solutes:
z.append(solute[1])
K_.append(ramp(phi_, [solute[2], solute[3]]))
beta_.append(ramp(phi_, [solute[4], solute[5]]))
dbeta.append(dramp([solute[4], solute[5]]))
if enable_EC:
rho_e = sum([c_e * z_e
for c_e, z_e in zip(c, z)]) # Sum of trial func.
rho_e_ = sum([c_e * z_e
for c_e, z_e in zip(c_, z)]) # Sum of curr. sol.
else:
rho_e_ = None
solvers = dict()
if enable_PF:
solvers["PF"] = setup_PF(w_["PF"], phi, g, psi, h, dx, ds, normal,
dirichlet_bcs["PF"], neumann_bcs,
boundary_to_mark, phi_1, u_1, M_1, c_1, V_1,
per_tau, sigma_bar, eps, dbeta, dveps,
enable_NS, enable_EC, use_iterative_solvers,
q_rhs)
if enable_EC:
solvers["EC"] = setup_EC(w_["EC"], c, V, b, U, rho_e, dx, ds, normal,
dirichlet_bcs["EC"], neumann_bcs,
boundary_to_mark, c_1, u_1, K_, veps_,
phi_flt_, solutes, per_tau, z, dbeta,
enable_NS, enable_PF, use_iterative_solvers,
q_rhs)
if enable_NS:
solvers["NS"] = setup_NS(w_["NS"], u, p, v, q, p0, q0, dx, ds, normal,
dirichlet_bcs["NS"], neumann_bcs,
boundary_to_mark, u_1, phi_flt_, rho_, rho_1,
g_, M_, mu_, rho_e_, c_, V_, c_1, V_1, dbeta,
solutes, per_tau, drho, sigma_bar, eps, dveps,
grav, fric, u_comoving, enable_PF, enable_EC,
use_iterative_solvers,
use_pressure_stabilization, p_lagrange, q_rhs)
return dict(solvers=solvers)
def unpack_quantities(surface_tension, grav_const, grav_dir, pf_mobility_coeff,
pf_mobility, interface_thickness, density, viscosity,
permittivity, trial_functions, test_functions, w_, w_1,
solutes, dt, enable_EC, enable_PF, enable_NS):
""" """
# Constant
sigma_bar = surface_tension * 3. / (2 * math.sqrt(2))
per_tau = df.Constant(1. / dt)
grav = df.Constant(tuple(grav_const * np.array(grav_dir)))
gamma = pf_mobility_coeff
eps = interface_thickness
rho_min = min(density) if enable_PF else density[0]
# Navier-Stokes
if enable_NS:
u = trial_functions["NSu"]
p = trial_functions["NSp"]
v = test_functions["NSu"]
q = test_functions["NSp"]
u_ = w_["NSu"]
p_ = w_["NSp"]
u_1 = w_1["NSu"]
p_1 = w_1["NSp"]
else:
u = p = v = q = None
u_ = p_ = None
u_1 = p_1 = None
# Phase field
if enable_PF:
phi, g = trial_functions["PF"]
psi, h = test_functions["PF"]
phi_, g_ = df.split(w_["PF"])
phi_1, g_1 = df.split(w_1["PF"])
else:
# Defaults to phase 1 if phase field is disabled
phi = 1.
g = psi = h = None
phi_ = phi_1 = 1.
g_ = g_1 = None
# Electrochemistry
if enable_EC:
num_solutes = len(trial_functions["EC"]) - 1
assert (num_solutes == len(solutes))
c = trial_functions["EC"][:num_solutes]
V = trial_functions["EC"][num_solutes]
b = test_functions["EC"][:num_solutes]
U = test_functions["EC"][num_solutes]
cV_ = df.split(w_["EC"])
cV_1 = df.split(w_1["EC"])
c_, V_ = cV_[:num_solutes], cV_[num_solutes]
c_1, V_1 = cV_1[:num_solutes], cV_1[num_solutes]
else:
c = V = b = U = c_ = V_ = c_1 = V_1 = None
phi_flt_ = unit_interval_filter(phi_)
phi_flt_1 = unit_interval_filter(phi_1)
# phi_flt_ = phi_
# phi_flt_1 = phi_1
#phi_ = phi_flt_
phi_1 = phi_flt_1
M_ = pf_mobility(phi_flt_, gamma)
M_1 = pf_mobility(phi_flt_1, gamma)
nu_ = ramp(phi_flt_, viscosity)
rho_ = ramp(phi_flt_, density)
veps_ = ramp(phi_flt_, permittivity)
rho_1 = ramp(phi_flt_1, density)
nu_1 = ramp(phi_flt_1, viscosity)
dveps = dramp(permittivity)
drho = dramp(density)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K_ = [] # Diffusivity K[species]
beta_ = [] # Conc. jump func. beta[species]
for solute in solutes:
z.append(solute[1])
K_.append(ramp_geometric(phi_flt_, [solute[2], solute[3]]))
beta_.append(ramp(phi_flt_, [solute[4], solute[5]]))
dbeta.append(dramp([solute[4], solute[5]]))
if enable_EC:
rho_e = sum([c_e * z_e for c_e, z_e in zip(c, z)])
rho_e_ = sum([c_e_ * z_e for c_e_, z_e in zip(c_, z)])
rho_e_1 = sum([c_e_1 * z_e for c_e_1, z_e in zip(c_1, z)])
else:
rho_e = rho_e_ = rho_e_1 = None
return (sigma_bar, per_tau, grav, gamma, eps, rho_min, u, p, v, q, u_, p_,
u_1, p_1, phi, g, psi, h, phi_, g_, phi_1, g_1, c, V, b, U, c_, V_,
c_1, V_1, phi_flt_, phi_flt_1, M_, M_1, nu_, rho_, veps_, rho_1,
nu_1, dveps, drho, dbeta, z, K_, beta_, rho_e, rho_e_, rho_e_1)
def setup(tstep, test_functions, trial_functions, w_, w_1, ds, dx, normal,
dirichlet_bcs, neumann_bcs, boundary_to_mark, permittivity, density,
viscosity, solutes, enable_PF, enable_EC, enable_NS, surface_tension,
dt, interface_thickness, grav_const, pf_mobility, pf_mobility_coeff,
use_iterative_solvers, use_pressure_stabilization, q_rhs,
**namespace):
""" Set up problem. """
# Constant
sigma_bar = surface_tension * 3. / (2 * math.sqrt(2))
per_tau = df.Constant(1. / dt)
grav = df.Constant((0., -grav_const))
gamma = pf_mobility_coeff
eps = interface_thickness
# Navier-Stokes
if enable_NS:
u = trial_functions["NSu"]
p = trial_functions["NSp"]
v = test_functions["NSu"]
q = test_functions["NSp"]
u_ = w_["NSu"]
p_ = w_["NSp"]
u_1 = w_1["NSu"]
p_1 = w_1["NSp"]
# Phase field
if enable_PF:
phi, g = trial_functions["PF"]
psi, h = test_functions["PF"]
phi_, g_ = df.split(w_["PF"])
phi_1, g_1 = df.split(w_1["PF"])
else:
# Defaults to phase 1 if phase field is disabled
phi_ = phi_1 = 1.
# Electrochemistry
if enable_EC:
num_solutes = len(trial_functions["EC"]) - 1
assert (num_solutes == len(solutes))
c = trial_functions["EC"][:num_solutes]
V = trial_functions["EC"][num_solutes]
b = test_functions["EC"][:num_solutes]
U = test_functions["EC"][num_solutes]
cV_ = df.split(w_["EC"])
cV_1 = df.split(w_1["EC"])
c_, V_ = cV_[:num_solutes], cV_[num_solutes]
c_1, V_1 = cV_1[:num_solutes], cV_1[num_solutes]
else:
c_, V_ = None, None
c_1, V_1 = None, None
M_ = pf_mobility(unit_interval_filter(phi_), gamma)
M_1 = pf_mobility(unit_interval_filter(phi_1), gamma)
nu_ = ramp(unit_interval_filter(phi_), viscosity)
rho_ = ramp(unit_interval_filter(phi_), density)
veps_ = ramp(unit_interval_filter(phi_), permittivity)
rho_1 = ramp(unit_interval_filter(phi_1), density)
dveps = dramp(permittivity)
drho = dramp(density)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K_ = [] # Diffusivity K[species]
beta_ = [] # Conc. jump func. beta[species]
for solute in solutes:
z.append(solute[1])
K_.append(ramp(phi_, [solute[2], solute[3]]))
beta_.append(ramp(phi_, [solute[4], solute[5]]))
dbeta.append(dramp([solute[4], solute[5]]))
if enable_EC:
rho_e = sum([c_e * z_e
for c_e, z_e in zip(c, z)]) # Sum of trial functions
rho_e_ = sum([c_e * z_e
for c_e, z_e in zip(c_, z)]) # Sum of current sol.
else:
rho_e = None
rho_e_ = None
if tstep == 0 and enable_NS:
solve_initial_pressure(w_["NSp"], p, q, u, v, dirichlet_bcs["NSp"], M_,
g_, phi_, rho_, rho_e_, V_, drho, sigma_bar,
eps, grav, dveps, enable_PF, enable_EC)
solvers = dict()
if enable_PF:
# solvers["PF"] = setup_PF(w_["PF"], phi, g, psi, h, dirichlet_bcs["PF"],
# phi_1, u_1, M_1, c_1, V_1,
# per_tau, sigma_bar, eps, dbeta, dveps,
# enable_NS, enable_EC,
# use_iterative_solvers)
solvers["PF"] = setup_PF(w_["PF"], phi, g, psi, h, dx, ds, normal,
dirichlet_bcs["PF"], neumann_bcs,
boundary_to_mark, phi_1, u_1, M_1, c_1, V_1,
per_tau, sigma_bar, eps, dbeta, dveps,
enable_NS, enable_EC, use_iterative_solvers,
q_rhs)
if enable_EC:
solvers["EC"] = setup_EC(w_["EC"], c, V, b, U, rho_e,
dirichlet_bcs["EC"], c_1, u_1, K_, veps_,
phi_, per_tau, z, dbeta, enable_NS, enable_PF,
use_iterative_solvers)
if enable_NS:
solvers["NSu"] = setup_NSu(u, v, u_, p_, dirichlet_bcs["NSu"], u_1,
p_1, phi_, rho_, rho_1, g_, M_, nu_, rho_e_,
V_, dt, drho, sigma_bar, eps, dveps, grav,
enable_PF, enable_EC)
solvers["NSp"] = setup_NSp(p, q, dirichlet_bcs["NSp"], u_, p_, p_1,
rho_, dt)
return dict(solvers=solvers)
def setup(test_functions, trial_functions, w_, w_1, bcs, permittivity, density,
viscosity, solutes, enable_PF, enable_EC, enable_NS, surface_tension,
dt, interface_thickness, grav_const, pf_mobility_coeff, pf_mobility,
use_iterative_solvers, **namespace):
""" Set up problem. """
# Constant
sigma_bar = surface_tension * 3. / (2 * math.sqrt(2))
per_tau = df.Constant(1. / dt)
grav = df.Constant((0., -grav_const))
gamma = pf_mobility_coeff
eps = interface_thickness
funs_ = df.split(w_["NSPFEC"])
funs_1 = df.split(w_1["NSPFEC"])
field_number = 0
if enable_NS:
v = test_functions["NSPFEC"][field_number]
u_ = funs_[field_number]
u_1 = funs_1[field_number]
field_number += 1
q = test_functions["NSPFEC"][field_number]
p_ = funs_[field_number]
p_1 = funs_1[field_number]
field_number += 1
if enable_PF:
psi = test_functions["NSPFEC"][field_number]
phi_ = funs_[field_number]
phi_1 = funs_1[field_number]
field_number += 1
h = test_functions["NSPFEC"][field_number]
g_ = funs_[field_number]
g_1 = funs_1[field_number]
field_number += 1
if enable_EC:
num_solutes = len(test_functions["NSPFEC"]) - field_number - 1
b = test_functions["NSPFEC"][field_number:(num_solutes + field_number)]
c_ = funs_[field_number:(num_solutes + field_number)]
c_1 = funs_1[field_number:(num_solutes + field_number)]
U = test_functions["NSPFEC"][num_solutes + field_number]
V_ = funs_[num_solutes + field_number]
V_1 = funs_1[num_solutes + field_number]
M_ = pf_mobility(phi_, gamma)
M_1 = pf_mobility(phi_1, gamma)
nu_ = ramp(phi_, viscosity)
nu_1 = ramp(phi_1, viscosity)
veps_ = ramp(phi_, permittivity)
veps_1 = ramp(phi_1, permittivity)
rho_ = ramp(phi_, density)
rho_1 = ramp(phi_1, density)
dveps = dramp(permittivity)
drho = dramp(density)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K_ = [] # Diffusivity K[species]
K_1 = []
beta_ = [] # Conc. jump func. beta[species]
beta_1 = []
for solute in solutes:
z.append(solute[1])
K_.append(ramp(phi_, [solute[2], solute[3]]))
K_1.append(ramp(phi_1, [solute[2], solute[3]]))
beta_.append(ramp(phi_, [solute[4], solute[5]]))
beta_1.append(ramp(phi_, [solute[4], solute[5]]))
dbeta.append(dramp([solute[4], solute[5]]))
if enable_EC:
rho_e_ = sum([c_e * z_e
for c_e, z_e in zip(c_, z)]) # Sum of curr. sol.
rho_e_1 = sum([c_e * z_e for c_e, z_e in zip(c_1, z)]) # prev sol.
solver = dict()
solver["NSPFEC"] = setup_NSPFEC(
w_["NSPFEC"], w_1["NSPFEC"], bcs["NSPFEC"], trial_functions["NSPFEC"],
v, q, psi, h, b, U, u_, p_, phi_, g_, c_, V_, u_1, p_1, phi_1, g_1,
c_1, V_1, M_, nu_, veps_, rho_, K_, rho_e_, M_1, nu_1, veps_1, rho_1,
K_1, rho_e_1, dbeta, dveps, drho, per_tau, sigma_bar, eps, grav, z,
enable_NS, enable_PF, enable_EC, use_iterative_solvers)
return dict(solvers=solver)
def method(ts, dt=0, extra_boundaries="", **kwargs):
""" Plot flux in time. """
info_cyan("Plot flux in time.")
params = ts.get_parameters()
steps = get_steps(ts, dt)
problem = params["problem"]
info("Problem: {}".format(problem))
boundary_to_mark, ds = fetch_boundaries(ts, problem, params,
extra_boundaries)
x_ = ts.functions()
if params["enable_NS"]:
u = x_["u"]
else:
u = df.Constant(0.)
if params["enable_PF"]:
phi = x_["phi"]
g = x_["g"]
exec("from problems.{} import pf_mobility".format(problem))
M = pf_mobility(phi, params["pf_mobility_coeff"])
else:
phi = 1.
g = df.Constant(0.)
M = df.Constant(0.)
solutes = params["solutes"]
c = []
c_grad_g_c = []
if params["enable_EC"]:
V = x_["V"]
else:
V = df.Constant(0.)
dbeta = [] # Diff. in beta
z = [] # Charge z[species]
K = [] # Diffusivity K[species]
beta = [] # Conc. jump func. beta[species]
for solute in solutes:
ci = x_[solute[0]]
dbetai = dramp([solute[4], solute[5]])
c.append(ci)
z.append(solute[1])
K.append(ramp(phi, [solute[2], solute[3]]))
beta.append(ramp(phi, [solute[4], solute[5]]))
dbeta.append(dbetai)
# THIS HAS NOT BEEN GENERALIZED!
c_grad_g_ci = df.grad(ci) + solute[1] * ci * df.grad(V)
if params["enable_PF"]:
c_grad_g_ci += dbetai * df.grad(phi)
c_grad_g_c.append(c_grad_g_ci)
nu = ramp(phi, params["viscosity"])
veps = ramp(phi, params["permittivity"])
rho = ramp(phi, params["density"])
dveps = dramp(params["permittivity"])
drho = dramp(params["density"])
t = np.zeros(len(steps))
# Define the fluxes
fluxes = dict()
fluxes["Velocity"] = u
fluxes["Phase"] = phi * u
fluxes["Mass"] = rho * x_["u"]
if params["enable_PF"]:
fluxes["Phase"] += -M * df.grad(g)
fluxes["Mass"] += -drho * M * df.grad(g)
if params["enable_EC"]:
for i, solute in enumerate(solutes):
fluxes["Solute {}".format(solute[0])] = K[i] * c_grad_g_c[i]
fluxes["E-field"] = -df.grad(V)
data = dict()
for boundary_name in boundary_to_mark:
data[boundary_name] = dict()
for flux_name in fluxes:
data[boundary_name][flux_name] = np.zeros(len(steps))
n = df.FacetNormal(ts.mesh)
for i, step in enumerate(steps):
info("Step {} of {}".format(step, len(ts)))
for field in x_:
ts.update(x_[field], field, step)
for boundary_name, (mark, k) in boundary_to_mark.items():
for flux_name, flux in fluxes.items():
data[boundary_name][flux_name][i] = df.assemble(
df.dot(flux, n) * ds[k](mark))
t[i] = ts.times[step]
savedata = dict()
flux_keys = sorted(fluxes.keys())
for boundary_name in boundary_to_mark:
savedata[boundary_name] = np.array(
list(
zip(
steps, t, *[
data[boundary_name][flux_name]
for flux_name in flux_keys
])))
if rank == 0:
header = "Step\tTime\t" + "\t".join(flux_keys)
for boundary_name in boundary_to_mark:
with open(
os.path.join(ts.analysis_folder,
"flux_in_time_{}.dat".format(boundary_name)),
"w") as outfile:
np.savetxt(outfile, savedata[boundary_name], header=header)