def create_bcs(Lx, Ly, Lx_inner,
solutes,
concentration_init,
mesh,
surface_charge,
enable_NS, enable_EC,
**namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(
right=[Right(Lx, Ly, Lx_inner)],
left=[Left(Lx, Ly, Lx_inner)],
#inner_wall=[InnerWall(Lx, Ly, Lx_inner)],
#outer_wall=[OuterWall(Lx, Ly, Lx_inner)]
wall=[Wall(Lx, Ly, Lx_inner)]
)
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
noslip = Fixed((0., 0.))
if enable_NS:
bcs["left"]["p"] = Pressure(0.)
bcs["right"]["p"] = Pressure(0.)
#bcs["inner_wall"]["u"] = noslip
#bcs["outer_wall"]["u"] = noslip
bcs["wall"]["u"] = noslip
if enable_EC:
bcs["left"]["V"] = Fixed(0.)
bcs["right"]["V"] = Charged(0.)
#bcs["right"]["V"] = Fixed(0.)
#bcs["outer_wall"]["V"] = Charged(0.)
#bcs["inner_wall"]["V"] = Charged(surface_charge)
bcs["wall"]["V"] = Charged(df.Expression(
"0.5*sigma_e*(tanh((x[0]-0.5*(Lx-Lx_inner))/delta)-"
"tanh((x[0]-0.5*(Lx+Lx_inner))/delta))",
sigma_e=surface_charge, delta=2., Lx=Lx, Lx_inner=Lx_inner,
degree=1))
for solute in solutes:
bcs["left"][solute[0]] = Fixed(concentration_init)
bcs["right"][solute[0]] = Fixed(concentration_init)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, mesh, surface_charge, enable_NS, enable_EC,
**namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(right=[Right(Lx)],
left=[Left(Lx)],
bottom=[Bottom(Ly)],
top=[Top(Ly)])
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
noslip = Fixed((0., 0.))
if enable_NS:
bcs["left"]["u"] = noslip
bcs["right"]["u"] = noslip
bcs["top"]["u"] = noslip
bcs["bottom"]["u"] = noslip
bcs_pointwise["p"] = (0., "x[0] < DOLFIN_EPS-{Lx}/2 && "
"x[1] < DOLFIN_EPS-{Ly}/2".format(Lx=Lx, Ly=Ly))
if enable_EC:
bcs["top"]["V"] = Fixed(0.)
bcs["bottom"]["V"] = Charged(surface_charge)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, velocity_top, solutes, concentration_init,
surface_charge, surface_potential, enable_NS, enable_PF,
enable_EC, **namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(top=[Top(Ly)], bottom=[Bottom()])
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
u_top = Fixed((velocity_top, 0.))
noslip = Fixed((0., 0.))
if enable_NS:
bcs["top"]["u"] = u_top
bcs["bottom"]["u"] = noslip
bcs_pointwise["p"] = (
0., "x[0] < DOLFIN_EPS && x[1] > {Ly}-DOLFIN_EPS".format(Ly=Ly))
if enable_EC:
for solute in solutes:
bcs["top"][solute[0]] = Fixed(concentration_init / abs(solute[1]))
bcs["top"]["V"] = Fixed(0.)
if surface_potential:
bcs["bottom"]["V"] = Fixed(surface_charge)
else:
bcs["bottom"]["V"] = Charged(surface_charge)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, solutes, surface_charge, enable_NS, enable_PF,
enable_EC, **namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(right=[Right(Lx)],
left=[Left(0)],
bottom=[Bottom(0)],
top=[Top(Ly)])
c0 = [1.0, 1.0]
noslip = Fixed((0., 0.))
V_ground = Fixed(0.0)
surfacecharge = Charged(surface_charge)
bcs = dict()
bcs_pointwise = dict()
bcs["right"] = dict()
bcs["left"] = dict()
bcs["top"] = dict()
bcs["bottom"] = dict()
if enable_NS:
bcs["right"]["u"] = noslip
bcs["left"]["u"] = noslip
bcs["top"]["u"] = noslip
bcs_pointwise["p"] = (0., "x[0] < DOLFIN_EPS && x[1] < DOLFIN_EPS")
if enable_EC:
bcs["top"]["V"] = surfacecharge
bcs["bottom"]["V"] = V_ground
for ci, solute in zip(c0, solutes):
bcs["bottom"][solute[0]] = Fixed(ci)
# Apply pointwise BCs e.g. to pin pressure.
return boundaries, bcs, bcs_pointwise
def create_bcs(
Lx,
Ly,
grid_spacing, # inlet_velocity,
concentration_init,
solutes,
surface_charge,
V_left,
V_right,
pressure_left,
pressure_right,
enable_NS,
enable_PF,
enable_EC,
**namespace):
""" The boundaries and boundary conditions are defined here. """
data = np.loadtxt("meshes/periodic_porous_dx" + str(grid_spacing) + ".dat")
centroids = data[:, :2]
rad = data[:, 2]
boundaries = dict(right=[Right(Lx)],
left=[Left(Lx)],
obstacles=[Obstacles(Lx, centroids, rad, grid_spacing)])
# Allocating the boundary dicts
bcs = dict()
bcs_pointwise = dict()
for boundary in boundaries:
bcs[boundary] = dict()
# u_inlet = Fixed((inlet_velocity, 0.))
noslip = Fixed((0., 0.))
p_inlet = Pressure(pressure_left)
p_outlet = Pressure(pressure_right)
phi_inlet = Fixed(-1.0)
phi_outlet = Fixed(1.0)
if enable_NS:
# bcs["left"]["u"] = u_inlet
bcs["obstacles"]["u"] = noslip
bcs["right"]["p"] = p_outlet
bcs["left"]["p"] = p_inlet
# bcs_pointwise["p"] = (0., "x[0] < -{Lx}/2+DOLFIN_EPS && x[1] > {Ly}/2-DOLFIN_EPS".format(Lx=Lx, Ly=Ly))
if enable_PF:
bcs["left"]["phi"] = phi_inlet
bcs["right"]["phi"] = phi_outlet
if enable_EC:
for solute in solutes:
bcs["left"][solute[0]] = Fixed(concentration_init)
# bcs["right"][solute[0]] = Fixed(0.)
bcs["left"]["V"] = Fixed(V_left)
bcs["right"]["V"] = Fixed(V_right)
bcs["obstacles"]["V"] = Charged(surface_charge)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, R, velocity_top, solutes, concentration_init,
surface_charge, V_left, V_right, pressure_left, pressure_right,
enable_NS, enable_PF, enable_EC, **namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(outer_narrowing=[OuterNarrowing(Lx, R)],
inner_narrowing=[InnerNarrowing(Lx, R)],
right=[Right(Lx)],
left=[Left(0)])
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
ground = Fixed(0.)
noslip = Fixed((0., 0.))
phi_inlet = Fixed(-1.0)
phi_outlet = Fixed(1.0)
p_inlet = Pressure(pressure_left)
p_outlet = Pressure(pressure_right)
if enable_NS:
bcs["inner_narrowing"]["u"] = noslip
bcs["outer_narrowing"]["u"] = noslip
bcs["left"]["p"] = p_inlet
bcs["right"]["p"] = p_outlet
#bcs_pointwise["p"] = (0., "x[0] < DOLFIN_EPS && x[1] > {Ly}-DOLFIN_EPS".format(Ly=Ly))
if enable_EC:
for solute in solutes:
bcs["left"][solute[0]] = Fixed(concentration_init)
bcs["right"][solute[0]] = Fixed(concentration_init)
bcs["left"]["V"] = Fixed(V_left)
bcs["right"]["V"] = Fixed(V_right)
bcs["outer_narrowing"]["V"] = Charged(0.0)
bcs["inner_narrowing"]["V"] = Charged(surface_charge)
#bcs_pointwise["V"] = (0., "x[0] < DOLFIN_EPS && x[1] > {Ly}-DOLFIN_EPS".format(Ly=Ly))
#if enable_PF:
bcs["left"]["phi"] = phi_inlet
bcs["right"]["phi"] = phi_inlet
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly,
grid_spacing, rad, num_obstacles,
surface_charge, solutes, enable_NS, enable_EC,
p_lagrange, V_lagrange,
concentration_init, V_left,
**namespace):
""" The boundaries and boundary conditions are defined here. """
data = np.loadtxt(
"meshes/periodic_porous_Lx{}_Ly{}_rad{}_N{}_dx{}.dat".format(
Lx, Ly, rad, num_obstacles, grid_spacing))
centroids = data[:, :2]
rad = data[:, 2]
boundaries = dict(
left=[Left(Lx, Ly)],
right=[Right(Lx, Ly)],
obstacles=[Obstacles(Lx, centroids, rad, grid_spacing)]
)
# Allocating the boundary dicts
bcs = dict()
bcs_pointwise = dict()
for boundary in boundaries:
bcs[boundary] = dict()
noslip = Fixed((0., 0.))
if enable_NS:
bcs["left"]["p"] = Pressure(0.)
bcs["right"]["p"] = Pressure(0.)
bcs["obstacles"]["u"] = noslip
if enable_EC:
for solute in solutes:
bcs["left"][solute[0]] = Fixed(concentration_init)
bcs["right"][solute[0]] = Fixed(concentration_init)
bcs["left"]["V"] = Fixed(V_left)
bcs["right"]["V"] = Charged(0.)
# bcs["right"]["V"] = Fixed(V_right)
bcs["obstacles"]["V"] = Charged(surface_charge)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, mesh, grid_spacing, rad, num_obstacles, surface_charge,
solutes, enable_NS, enable_EC, p_lagrange, V_lagrange,
**namespace):
""" The boundaries and boundary conditions are defined here. """
data = np.loadtxt(
"meshes/periodic_porous_Lx{}_Ly{}_rad{}_N{}_dx{}.dat".format(
Lx, Ly, rad, num_obstacles, grid_spacing))
centroids = data[:, :2]
rad = data[:, 2]
# Find a single node to pin pressure to
x_loc = np.array(mesh.coordinates())
x_proc = np.zeros((size, 2))
ids_notboun = np.logical_and(
x_loc[:, 0] > x_loc[:, 0].min() + df.DOLFIN_EPS,
x_loc[:, 1] > x_loc[:, 1].min() + df.DOLFIN_EPS)
x_loc = x_loc[ids_notboun, :]
d2 = (x_loc[:, 0] + Lx / 2)**2 + (x_loc[:, 1] + Ly / 2)**2
x_bottomleft = x_loc[d2 == d2.min()][0]
x_proc[rank, :] = x_bottomleft
x_pin = np.zeros_like(x_proc)
comm.Allreduce(x_proc, x_pin, op=MPI.SUM)
x_pin = x_pin[x_pin[:, 0] == x_pin[:, 0].min(), :][0]
info("Pinning point: {}".format(x_pin))
pin_code = ("x[0] < {x}+{eps} && "
"x[0] > {x}-{eps} && "
"x[1] > {y}-{eps} && "
"x[1] < {y}+{eps}").format(x=x_pin[0], y=x_pin[1], eps=1e-3)
boundaries = dict(obstacles=[Obstacles(Lx, centroids, rad, grid_spacing)])
# Allocating the boundary dicts
bcs = dict()
bcs_pointwise = dict()
for boundary in boundaries:
bcs[boundary] = dict()
noslip = Fixed((0., 0.))
if enable_NS:
bcs["obstacles"]["u"] = noslip
if not p_lagrange:
bcs_pointwise["p"] = (0., pin_code)
if enable_EC:
bcs["obstacles"]["V"] = Charged(surface_charge)
if not V_lagrange:
bcs_pointwise["V"] = (0., pin_code)
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, surface_charge_top, surface_charge_bottom, enable_NS,
enable_PF, enable_EC, **namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(top=[Top(Ly)], bottom=[Bottom()])
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
noslip = Fixed((0., 0.))
if enable_NS:
bcs["top"]["u"] = noslip
bcs["bottom"]["u"] = noslip
bcs_pointwise["p"] = (0., "x[0] < DOLFIN_EPS && x[1] < DOLFIN_EPS")
if enable_EC:
bcs["top"]["V"] = Charged(surface_charge_top)
bcs["bottom"]["V"] = Charged(surface_charge_bottom)
bcs_pointwise["V"] = (0., "x[0] < DOLFIN_EPS && x[1] < DOLFIN_EPS")
return boundaries, bcs, bcs_pointwise
def create_bcs(Lx, Ly, solutes, concentration_init, surface_charge,
pressure_left, pressure_right, enable_NS, enable_PF, enable_EC,
**namespace):
""" The boundaries and boundary conditions are defined here. """
boundaries = dict(
inner=[Inner(Lx, Ly)],
bottom=[Bottom()],
top=[Top(Ly)],
left=[Left()],
right=[Right(Lx)],
)
bcs = dict()
for boundary_name in boundaries.keys():
bcs[boundary_name] = dict()
# Apply pointwise BCs e.g. to pin pressure.
bcs_pointwise = dict()
noslip = Fixed((0., 0.))
phi_inlet = Fixed(-1.0)
p_inlet = Pressure(pressure_left)
p_outlet = Pressure(pressure_right)
if enable_NS:
bcs["top"]["u"] = noslip
bcs["bottom"]["u"] = noslip
bcs["inner"]["u"] = noslip
bcs["left"]["p"] = p_inlet
bcs["right"]["p"] = p_outlet
#bcs_pointwise["p"] = (0., "x[0] < DOLFIN_EPS && x[1] < DOLFIN_EPS")
# bcs["outer"]["p"] = Pressure(0.)
if enable_EC:
for solute in solutes:
bcs["left"][solute[0]] = Fixed(concentration_init)
bcs["right"][solute[0]] = Fixed(concentration_init)
bcs["top"]["V"] = Fixed(0.)
bcs["bottom"]["V"] = Fixed(0.)
bcs["left"]["V"] = Fixed(0.)
bcs["right"]["V"] = Fixed(0.)
bcs["inner"]["V"] = Charged(surface_charge)
if enable_PF:
bcs["left"]["phi"] = phi_inlet
#bcs["right"]["phi"] = phi_inlet
return boundaries, bcs, bcs_pointwise
