def setup(self, state):
if not self._initialised:
# check geometric dimension is 3D
if state.mesh.geometric_dimension() != 3:
raise ValueError(
'Spherical components only work when the geometric dimension is 3!'
)
space = FunctionSpace(state.mesh, "CG", 1)
super().setup(state, space=space)
V = VectorFunctionSpace(state.mesh, "CG", 1)
self.x, self.y, self.z = SpatialCoordinate(state.mesh)
self.x_hat = Function(V).interpolate(
Constant(as_vector([1.0, 0.0, 0.0])))
self.y_hat = Function(V).interpolate(
Constant(as_vector([0.0, 1.0, 0.0])))
self.z_hat = Function(V).interpolate(
Constant(as_vector([0.0, 0.0, 1.0])))
self.R = sqrt(self.x**2 + self.y**2) # distance from z axis
self.r = sqrt(self.x**2 + self.y**2 +
self.z**2) # distance from origin
self.f = state.fields(self.fname)
if np.prod(self.f.ufl_shape) != 3:
raise ValueError(
'Components can only be found of a vector function space in 3D.'
)
def update_constants(self):
"""
Update p and q constants from true peakon data.
"""
self.p.assign(self.true_peakon_file['p'][self.outputting.t_idx] * 0.5 *
(1 + exp(-self.Ld / sqrt(self.alphasq))) /
(1 - exp(-self.Ld / sqrt(self.alphasq))))
self.q.assign(self.true_peakon_file['q'][self.outputting.t_idx])
def max_courant_number(self, u, dt):
if not hasattr(self, "_area"):
V = FunctionSpace(u.function_space().mesh(), "DG", 0)
expr = TestFunction(V) * dx
self._area = assemble(expr)
self.Courant = Function(V)
self.Courant.project(sqrt(inner(u, u)) / sqrt(self._area) * dt)
return self.Courant.dat.data.max()
def get_true_sol_expr(spatial_coord, kappa):
if mesh_dim == 3:
x, y, z = spatial_coord
norm = sqrt(x**2 + y**2 + z**2)
return Constant(1j / (4 * pi)) / norm * exp(1j * kappa * norm)
elif mesh_dim == 2:
x, y = spatial_coord
return Constant(1j / 4) * hankel_function(kappa * sqrt(x**2 + y**2),
n=hankel_cutoff)
raise ValueError("Only meshes of dimension 2, 3 supported")
def _K(self):
"""
Create the function that defines the conductivity.
Returns:
Function: The Spitzer-Harm conductivity
"""
tmp = 288 * pi * sqrt(2) * epsilon_0**2 / sqrt(e * m_e)
tmp = tmp * pow(self.T, 5 / 2) / (self.coulomb_ln * self.ionisation)
return tmp
def get_true_sol_expr(spatial_coord, wave_number):
mesh_dim = len(spatial_coord)
if mesh_dim == 3:
x, y, z = spatial_coord
norm = sqrt(x**2 + y**2 + z**2)
return Constant(1j / (4 * pi)) / norm * exp(1j * wave_number * norm)
elif mesh_dim == 2:
x, y = spatial_coord
return Constant(1j / 4) * hankel_function(
wave_number * sqrt(x**2 + y**2), n=80)
raise ValueError("Only meshes of dimension 2, 3 supported")
def run_advection_diffusion(tmpdir):
# Mesh, state and equation
L = 10
mesh = PeriodicIntervalMesh(20, L)
dt = 0.02
tmax = 1.0
diffusion_params = DiffusionParameters(kappa=0.75, mu=5)
output = OutputParameters(dirname=str(tmpdir), dumpfreq=25)
state = State(mesh, dt=dt, output=output)
V = state.spaces("DG", "DG", 1)
Vu = VectorFunctionSpace(mesh, "CG", 1)
equation = AdvectionDiffusionEquation(
state, V, "f", Vu=Vu, diffusion_parameters=diffusion_params)
problem = [(equation, ((SSPRK3(state), transport), (BackwardEuler(state),
diffusion)))]
# Initial conditions
x = SpatialCoordinate(mesh)
xc_init = 0.25 * L
xc_end = 0.75 * L
umax = 0.5 * L / tmax
# Get minimum distance on periodic interval to xc
x_init = conditional(
sqrt((x[0] - xc_init)**2) < 0.5 * L, x[0] - xc_init,
L + x[0] - xc_init)
x_end = conditional(
sqrt((x[0] - xc_end)**2) < 0.5 * L, x[0] - xc_end, L + x[0] - xc_end)
f_init = 5.0
f_end = f_init / 2.0
f_width_init = L / 10.0
f_width_end = f_width_init * 2.0
f_init_expr = f_init * exp(-(x_init / f_width_init)**2)
f_end_expr = f_end * exp(-(x_end / f_width_end)**2)
state.fields('f').interpolate(f_init_expr)
state.fields('u').interpolate(as_vector([Constant(umax)]))
f_end = state.fields('f_end', V).interpolate(f_end_expr)
# Time stepper
timestepper = PrescribedTransport(state, problem)
timestepper.run(0, tmax=tmax)
error = norm(state.fields('f') - f_end) / norm(f_end)
return error
def write_output(diag, t, counter, dfr, nc_h5_dfr, outf, outf_ll, fld_out,
fld_out_ll):
"""Function to write vtu, txt output"""
# Update and output diagnostics
energy = e_form(un, Dn)
En.interpolate(energy)
if 'Energy' in diag.keys():
diag['Energy'] = assemble(energy * dx)
if 'Mass' in diag.keys():
diag['Mass'] = assemble(Dn * dx)
if 'Enstrophy' in diag.keys():
diag['Enstrophy'] = assemble(qn**2 * Dn * dx)
if 'L2_error_D' in diag.keys():
diag['L2_error_D'] = sqrt(assemble((Dn - D0) * (Dn - D0) * dx))
if 'L2_error_u' in diag.keys():
diag['L2_error_u'] = sqrt(assemble(inner(un - u0, un - u0) * dx))
_c = 0
for k in diag:
nc_temp[counter % nc_h5_dfr][_c] = diag[k]
_c += 1
# Save I/O time by not writing at each timestep
if (counter % nc_h5_dfr) == nc_h5_dfr - 1:
if COMM_WORLD.Get_rank() == 0:
print("Timestep nr", counter, ": Writing nc files at", ctime())
write_to_nc_file(t, nc_temp)
if nc_safe:
write_to_nc_file(t, nc_temp, '_bckp')
# Write to checkpoint
chkpt.store(xn)
chkpt.write_attribute("/", "time", t)
if h5_safe:
chkpt_bckp.store(xn)
chkpt_bckp.write_attribute("/", "time", t)
# Output vtu file
if t in field_dumptimes:
#q2Dn.project(qn**2*Dn)
#eta_out.interpolate(Dn + b)
#vortsolver.solve()
u_err.assign(un - u0)
D_err.assign(Dn - D0)
q_err.assign(qn - q0)
outf.write(*fld_out)
if write_latlon:
outf_ll.write(*fld_out_ll)
def norm(u, norm_type="L2"):
r"""Compute the norm of a field
Computes one of any number of norms of a scalar or vector field. The
available options are:
- ``L2``: :math:`\|u\|^2 = \int_\Omega|u|^2dx`
- ``H01``: :math:`\|u\|^2 = \int_\Omega|\nabla u|^2dx`
- ``H1``: :math:`\|u\|^2 = \int_\Omega\left(|u|^2 + L^2|\nabla u|^2\right)dx`
- ``L1``: :math:`\|u\| = \int_\Omega|u|dx`
- ``TV``: :math:`\|u\| = \int_\Omega|\nabla u|dx`
- ``Linfty``: :math:`\|u\| = \max_{x\in\Omega}|u(x)|`
The extra factor :math:`L` in the :math:`H^1` norm is the diameter of
the domain in the infinity metric. This extra factor is included to
make the norm scale appropriately with the size of the domain.
"""
if norm_type == "L2":
form, p = inner(u, u) * dx, 2
if norm_type == "H01":
form, p = inner(grad(u), grad(u)) * dx, 2
if norm_type == "H1":
L = utilities.diameter(u.ufl_domain())
form, p = inner(u, u) * dx + L**2 * inner(grad(u), grad(u)) * dx, 2
if norm_type == "L1":
form, p = sqrt(inner(u, u)) * dx, 1
if norm_type == "TV":
form, p = sqrt(inner(grad(u), grad(u))) * dx, 1
if norm_type == "Linfty":
data = u.dat.data_ro
if len(data.shape) == 1:
local_max = np.max(np.abs(data))
elif len(data.shape) == 2:
local_max = np.max(np.sqrt(np.sum(data**2, 1)))
return u.comm.allreduce(local_max, op=max)
return assemble(form)**(1 / p)
def _plot_2d_field(method_name,
function,
*args,
complex_component="real",
**kwargs):
axes = kwargs.pop("axes", None)
if axes is None:
figure = plt.figure()
axes = figure.add_subplot(111)
if len(function.ufl_shape) == 1:
mesh = function.ufl_domain()
element = function.ufl_element().sub_elements()[0]
Q = FunctionSpace(mesh, element)
function = interpolate(sqrt(inner(function, function)), Q)
num_sample_points = kwargs.pop("num_sample_points", 10)
coords, vals, triangles = _two_dimension_triangle_func_val(
function, num_sample_points)
coords = toreal(coords, "real")
x, y = coords[:, 0], coords[:, 1]
triangulation = matplotlib.tri.Triangulation(x, y, triangles=triangles)
method = getattr(axes, method_name)
return method(triangulation, toreal(vals, complex_component), *args,
**kwargs)
def _plot_2d_field(method_name,
function,
*args,
complex_component="real",
**kwargs):
axes = kwargs.pop("axes", None)
if axes is None:
figure = plt.figure()
axes = figure.add_subplot(111)
Q = function.function_space()
mesh = Q.mesh()
if len(function.ufl_shape) == 1:
element = function.ufl_element().sub_elements()[0]
Q = FunctionSpace(mesh, element)
function = interpolate(sqrt(inner(function, function)), Q)
num_sample_points = kwargs.pop("num_sample_points", 10)
function_plotter = FunctionPlotter(mesh, num_sample_points)
triangulation = function_plotter.triangulation
values = function_plotter(function)
method = getattr(axes, method_name)
return method(triangulation, toreal(values, complex_component), *args,
**kwargs)
def referencemesh(mesh, b, hinitial, Href):
'''In-place modification of an extruded mesh to create the reference mesh.
Changes the top surface to lambda = b + sqrt(Href^2 + (Hinitial - b)^2).
Assumes b,hinitial are Functions defined on the base mesh. Assumes the
input mesh is extruded 3D mesh with 0 <= z <= 1.'''
if not _admissible(b, hinitial):
assert ValueError('input hinitial not admissible')
P1base = fd.FunctionSpace(mesh._base_mesh, 'P', 1)
HH = fd.Function(P1base).interpolate(hinitial - b)
# alternative:
#lambase = fd.Function(P1base).interpolate(b + fd.max_value(Href, Hstart))
lambase = fd.Function(P1base).interpolate(b + fd.sqrt(HH**2 + Href**2))
lam = extend(mesh, lambase)
Vcoord = mesh.coordinates.function_space()
if mesh._base_mesh.cell_dimension() == 1:
x, z = fd.SpatialCoordinate(mesh)
XX = fd.Function(Vcoord).interpolate(fd.as_vector([x, lam * z]))
elif mesh._base_mesh.cell_dimension() == 2:
x, y, z = fd.SpatialCoordinate(mesh)
XX = fd.Function(Vcoord).interpolate(fd.as_vector([x, y, lam * z]))
else:
raise ValueError('only 2D and 3D reference meshes are generated')
mesh.coordinates.assign(XX)
return 0
def Bueler_profile(mesh, R):
x, y = firedrake.SpatialCoordinate(mesh)
r = firedrake.sqrt(x**2 + y**2)
h_divide = (2 * R * (alpha/A0)**(1/n) * (n-1)/n)**(n/(2*n+2))
h_part2 = (n+1)*(r/R) - n*(r/R)**((n+1)/n) + n*(max_value(1-(r/R),0))**((n+1)/n) - 1
h_expr = (h_divide/((n-1)**(n/(2*n+2)))) * (max_value(h_part2,0))**(n/(2*n+2))
return h_expr
def equation(z):
Z = z.function_space()
φ, v = firedrake.TestFunctions(Z)
h, q = firedrake.split(z)
F_h, F_q = _fluxes(h, q, g)
mesh = Z.mesh()
n = firedrake.FacetNormal(mesh)
c = abs(inner(q / h, n)) + sqrt(g * h)
sources = -inner(g * h * grad(b), v) * dx
fluxes = (forms.cell_flux(F_h, φ) + forms.central_facet_flux(F_h, φ) +
forms.lax_friedrichs_facet_flux(h, c, φ) +
forms.cell_flux(F_q, v) + forms.central_facet_flux(F_q, v) +
forms.lax_friedrichs_facet_flux(q, c, v))
boundary_ids = set(mesh.exterior_facets.unique_markers)
wall_ids = tuple(boundary_ids - set(outflow_ids) - set(inflow_ids))
q_wall = q - 2 * inner(q, n) * n
boundary_fluxes = (
_boundary_flux(z, h, q, g, outflow_ids) +
_boundary_flux(z, h_in, q_in, g, inflow_ids) +
_boundary_flux(z, h, q_wall, g, wall_ids) +
forms.lax_friedrichs_boundary_flux(h, h, c, φ, outflow_ids) +
forms.lax_friedrichs_boundary_flux(q, q, c, v, outflow_ids) +
forms.lax_friedrichs_boundary_flux(h, h_in, c, φ, inflow_ids) +
forms.lax_friedrichs_boundary_flux(q, q_in, c, v, inflow_ids) +
forms.lax_friedrichs_boundary_flux(h, h, c, φ, wall_ids) +
forms.lax_friedrichs_boundary_flux(q, q_wall, c, v, wall_ids))
return sources - fluxes - boundary_fluxes
def trisurf(function, *args, **kwargs):
r"""Create a 3D surface plot of a 2D Firedrake :class:`~.Function`
If the input function is a vector field, the magnitude will be plotted.
:arg function: the Firedrake :class:`~.Function` to plot
:arg args: same as for matplotlib :meth:`plot_trisurf <mpl_toolkits.mplot3d.axes3d.Axes3D.plot_trisurf>`
:arg kwargs: same as for matplotlib
:return: matplotlib :class:`Poly3DCollection <mpl_toolkits.mplot3d.art3d.Poly3DCollection>` object
"""
axes = kwargs.pop("axes", None)
if axes is None:
figure = plt.figure()
axes = figure.add_subplot(111, projection='3d')
_kwargs = {"antialiased": False, "edgecolor": "none",
"cmap": plt.rcParams["image.cmap"]}
_kwargs.update(kwargs)
mesh = function.ufl_domain()
if mesh.geometric_dimension() == 3:
return _trisurf_3d(axes, function, *args, **_kwargs)
if len(function.ufl_shape) == 1:
element = function.ufl_element().sub_elements()[0]
Q = FunctionSpace(mesh, element)
function = interpolate(sqrt(inner(function, function)), Q)
num_sample_points = kwargs.pop("num_sample_points", 10)
coords, vals, triangles = _two_dimension_triangle_func_val(function,
num_sample_points)
x, y = coords[:, 0], coords[:, 1]
triangulation = matplotlib.tri.Triangulation(x, y, triangles=triangles)
_kwargs.update({"shade": False})
return axes.plot_trisurf(triangulation, vals, *args, **_kwargs)
def _K_min(self):
r_ii = (3 / (4 * pi * self.ion_density))**(1 / 3)
tau_min = r_ii / self.v_th
tmp = 48 * self.ionisation * self.ion_density * e**2 * self.T * tau_min
tmp = tmp / sqrt(pi) / m_e
return tmp
def create_conductivity(mesh, V, T):
"""
This is the conductivity term.
Here we use the spitzer-harm conductivity.
mesh: Mesh, The mesh to define the function for.
V: FunctionSpace, The function space that the function should be in
T: Function, The temperature of the plasma.
"""
coulomb_ln = create_coulomb_ln(mesh, V)
Z = create_Z(mesh, V)
tmp = 288 * pi * sqrt(2) * epsilon_0**2 / sqrt(e * m_e)
tmp = tmp * pow(T, 5 / 2) / (coulomb_ln * Z)
return tmp
def latlon_coords(mesh):
x0, y0, z0 = SpatialCoordinate(mesh)
unsafe = z0 / sqrt(x0 * x0 + y0 * y0 + z0 * z0)
safe = Min(Max(unsafe, -1.0), 1.0) # avoid silly roundoff errors
theta = asin(safe) # latitude
lamda = atan_2(y0, x0) # longitude
return theta, lamda
def setup_solver(self, up_init=None):
""" Setup the solvers
"""
self.up0 = Function(self.W)
if up_init is not None:
chk_in = checkpointing.HDF5File(up_init, file_mode='r')
chk_in.read(self.up0, "/up")
chk_in.close()
self.u0, self.p0 = split(self.up0)
self.up = Function(self.W)
if up_init is not None:
chk_in = checkpointing.HDF5File(up_init, file_mode='r')
chk_in.read(self.up, "/up")
chk_in.close()
self.u1, self.p1 = split(self.up)
self.up.sub(0).rename("velocity")
self.up.sub(1).rename("pressure")
v, q = TestFunctions(self.W)
h = CellVolume(self.mesh)
u_norm = sqrt(dot(self.u0, self.u0))
if self.has_nullspace:
nullspace = MixedVectorSpaceBasis(
self.W,
[self.W.sub(0), VectorSpaceBasis(constant=True)])
else:
nullspace = None
tau = ((2.0 / self.dt)**2 + (2.0 * u_norm / h)**2 +
(4.0 * self.nu / h**2)**2)**(-0.5)
# temporal discretization
F = (1.0 / self.dt) * inner(self.u1 - self.u0, v) * dx
# weak form
F += (+inner(dot(self.u0, nabla_grad(self.u1)), v) * dx +
self.nu * inner(grad(self.u1), grad(v)) * dx -
(1.0 / self.rho) * self.p1 * div(v) * dx +
div(self.u1) * q * dx - inner(self.forcing, v) * dx)
# residual form
R = (+(1.0 / self.dt) * (self.u1 - self.u0) +
dot(self.u0, nabla_grad(self.u1)) - self.nu * div(grad(self.u1)) +
(1.0 / self.rho) * grad(self.p1) - self.forcing)
# GLS
F += tau * inner(
+dot(self.u0, nabla_grad(v)) - self.nu * div(grad(v)) +
(1.0 / self.rho) * grad(q), R) * dx
self.problem = NonlinearVariationalProblem(F, self.up, self.bcs)
self.solver = NonlinearVariationalSolver(
self.problem,
nullspace=nullspace,
solver_parameters=self.solver_parameters)
def eigenvalues(a):
r"""Return a pair of symbolic expressions for the largest and smallest
eigenvalues of a 2D rank-2 tensor"""
tr_a = tr(a)
det_a = det(a)
# TODO: Fret about numerical stability
Δ = sqrt(tr_a**2 - 4 * det_a)
return ((tr_a + Δ) / 2, (tr_a - Δ) / 2)
def stresses(ε_x, ε_z, A):
r"""Calculate the membrane and vertical shear stresses for the given
horizontal and shear strain rates and fluidity"""
I = Identity(2)
tr = trace(ε_x)
ε_e = sqrt((inner(ε_x, ε_x) + inner(ε_z, ε_z) + tr**2) / 2)
μ = 0.5 * A**(-1 / n) * ε_e**(1 / n - 1)
return 2 * μ * (ε_x + tr * I), 2 * μ * ε_z
def __init__(self, state, V, direction=[], supg_params=None):
super(SUPGAdvection, self).__init__(state)
dt = state.timestepping.dt
params = supg_params.copy() if supg_params else {}
params.setdefault('a0', dt/sqrt(15.))
params.setdefault('a1', dt/sqrt(15.))
gamma = TestFunction(V)
theta = TrialFunction(V)
self.theta0 = Function(V)
# make SUPG test function
taus = [params["a0"], params["a1"]]
for i in direction:
taus[i] = 0.0
tau = Constant(((taus[0], 0.), (0., taus[1])))
dgamma = dot(dot(self.ubar, tau), grad(gamma))
gammaSU = gamma + dgamma
n = FacetNormal(state.mesh)
un = 0.5*(dot(self.ubar, n) + abs(dot(self.ubar, n)))
a_mass = gammaSU*theta*dx
arhs = a_mass - dt*gammaSU*dot(self.ubar, grad(theta))*dx
if 1 in direction:
arhs -= (
dt*dot(jump(gammaSU), (un('+')*theta('+')
- un('-')*theta('-')))*dS_v
- dt*(gammaSU('+')*dot(self.ubar('+'), n('+'))*theta('+')
+ gammaSU('-')*dot(self.ubar('-'), n('-'))*theta('-'))*dS_v
)
if 2 in direction:
arhs -= (
dt*dot(jump(gammaSU), (un('+')*theta('+')
- un('-')*theta('-')))*dS_h
- dt*(gammaSU('+')*dot(self.ubar('+'), n('+'))*theta('+')
+ gammaSU('-')*dot(self.ubar('-'), n('-'))*theta('-'))*dS_h
)
self.theta1 = Function(V)
self.dtheta = Function(V)
problem = LinearVariationalProblem(a_mass, action(arhs,self.theta1), self.dtheta)
self.solver = LinearVariationalSolver(problem,
options_prefix='SUPGAdvection')
def M(ε, A):
r"""Calculate the membrane stress for a given strain rate and
fluidity"""
I = Identity(2)
tr_ε = trace(ε)
ε_e = sqrt((inner(ε, ε) + tr_ε**2) / 2)
μ = 0.5 * A**(-1 / n) * ε_e**(1 / n - 1)
return 2 * μ * (ε + tr_ε * I)
class CompressibleEadyParameters(CompressibleParameters, EadyParameters):
"""
Physical parameters for Compressible Eady
"""
g = 10.
N = sqrt(EadyParameters.Nsq)
theta_surf = 300.
dthetady = theta_surf / g * EadyParameters.dbdy
Pi0 = 0.0
def profilePlots(t, plotData, u, s, h, zb, zF, melt, Q, first=False):
'''Plot profiles every nYears/20
'''
# Return if not ready for plot
if t < plotData['nextProfPlotTime'] or plotData['axesP'] is None \
and not first:
return
# Increment time for next plot: use max to kill initial -1
plotData['nextProfPlotTime'] = max(plotData['nextProfPlotTime'], 0.)
plotData['nextProfPlotTime'] += plotData['profileDT']
myColor = plotData['cmap'][plotData['profNum']]
myLabel = f'year={t:.1f}'
# First is special case
if first:
myColor = 'k'
zbProf = [zb((xy[0], xy[1])) for xy in plotData['profXY']]
plotData['axesP'][1].plot(plotData['distance'], zbProf, color=myColor)
myLabel = 'initial'
zFProf = [zF((xy[0], xy[1])) for xy in plotData['profXY']]
plotData['axesP'][1].plot(plotData['distance'], zFProf, color='b')
# Now do plots
speed = firedrake.interpolate(firedrake.sqrt(firedrake.inner(u, u)), Q)
speedProf = [speed((xy[0], xy[1])) for xy in plotData['profXY']]
plotData['axesP'][0].plot(plotData['distance'],
speedProf,
label=myLabel,
color=myColor)
plotData['axesP'][0].legend(ncol=2)
# Geometry
sProf = [s((xy[0], xy[1])) for xy in plotData['profXY']]
bProf = [
s((xy[0], xy[1])) - h((xy[0], xy[1])) for xy in plotData['profXY']
]
zbProf = [zb((xy[0], xy[1])) for xy in plotData['profXY']]
plotData['axesP'][1].plot(plotData['distance'], sProf, color=myColor)
plotData['axesP'][1].plot(plotData['distance'], bProf, color=myColor)
plotData['axesP'][1].plot(plotData['distance'], zbProf, color='k')
#
if melt is not None:
meltProf = [melt((xy[0], xy[1])) for xy in plotData['profXY']]
plotData['axesP'][2].plot(plotData['distance'],
meltProf,
label=myLabel,
color=myColor)
hProf = np.array([h((xy[0], xy[1])) for xy in plotData['profXY']])
dhdt = (hProf - plotData['lasth']) / plotData['profileDT']
plotData['axesP'][3].plot(plotData['distance'],
dhdt,
label=myLabel,
color=myColor)
plotData['lasth'] = hProf
plotData['profNum'] += 1
# plt.draw()
if plotData['plotResult']:
plotData['figP'].canvas.draw()
def violation(self):
gradSv = self.gradS.vector()[:]
av = self.upper_bound.vector()[:]
violv = self.viol.vector()[:].copy()
for i in range(len(gradSv)):
W, Sigma, V = svd(gradSv[i], full_matrices=False)
for j in range(self.dim):
Sigma[j] = max(Sigma[j] - av[i], 0)**2
violv[i] = self.c * 0.5 * np.sum(Sigma)
self.viol.vector().set_local(violv.flatten())
return fd.sqrt(fd.assemble(self.viol * fd.dx))
def betaInit(s, h, speed, V, Q, Q1, grounded, inversionParams):
"""Compute intitial beta using 0.5 taud.
Parameters
----------
s : firedrake function
model surface elevation
h : firedrake function
model thickness
speed : firedrake function
modelled speed
V : firedrake vector function space
vector function space
Q : firedrake function space
scalar function space
grounded : firedrake function
Mask with 1s for grounded 0 for floating.
"""
# Use a result from prior inversion
checkFile = inversionParams['initFile']
Quse = Q
if inversionParams['initWithDeg1']:
checkFile = f'{inversionParams["inversionResult"]}.deg1'
Quse = Q1
if checkFile is not None:
betaTemp = mf.getCheckPointVars(checkFile, 'betaInv', Quse)['betaInv']
beta1 = icepack.interpolate(betaTemp, Q)
return beta1
# No prior result, so use fraction of taud
tauD = firedrake.project(-rhoI * g * h * grad(s), V)
#
stress = firedrake.sqrt(firedrake.inner(tauD, tauD))
Print('stress', firedrake.assemble(stress * firedrake.dx))
fraction = firedrake.Constant(0.95)
U = max_value(speed, 1)
C = fraction * stress / U**(1/m)
if inversionParams['friction'] == 'schoof':
mExp = 1/m + 1
U0 = firedrake.Constant(inversionParams['uThresh'])
C = C * (m/(m+1)) * (U0**mExp + U**mExp)**(1/(m+1))
beta = firedrake.interpolate(firedrake.sqrt(C) * grounded, Q)
return beta
def friction(**kwargs):
keys = ('velocity', 'thickness', 'surface', 'friction')
u, h, s, C = map(kwargs.get, keys)
p_W = ρ_W * g * max_value(0, -(s - h))
p_I = ρ_I * g * h
N = p_I - p_W
τ_c = N / 2
u_c = (τ_c / C)**m
u_b = sqrt(inner(u, u))
return τ_c * ((u_c**(1 / m + 1) + u_b**(1 / m + 1))**(m / (m + 1)) - u_c)
def getModelVelocity(baseName, Q, V, minSigma=5, maxSigma=100):
"""Read in a tiff velocity data set and return
firedrake interpolate functions.
Parameters
----------
baseName : str
baseName should be of the form pattern.*.abc or pattern
The wildcard (*) will be filled with the suffixes (vx, vy.)
e.g.,pattern.vx.abc.tif, pattern.vy.abc.tif.
Q : firedrake function space
function space
V : firedrake vector space
vector space
Returns
-------
uObs firedrake interp function on V
velocity (m/yr)
speed firedrake interp function on Q
speed in (m)
sigmaX firedrake interp function on Q
vx error (m)
sigmaY firedrake interp function on Q
vy error (m)
"""
# suffixes for products used
suffixes = ['vx', 'vy', 'ex', 'ey']
rasters = {}
# prep baseName - baseName.*.xyz.tif or baseName.*
if '*' not in baseName:
baseName += '.*'
if '.tif' not in baseName:
baseName += '.tif'
# read data
for suffix in suffixes:
myBand = baseName.replace('*', suffix)
if not os.path.exists(myBand):
u.myerror(f'Velocity/error file - {myBand} - does not exist')
rasters[suffix] = rasterio.open(myBand, 'r')
# Firedrake interpolators
uObs = icepack.interpolate((rasters['vx'], rasters['vy']), V)
# force error to be at least 1 to avoid 0 or negatives.
sigmaX = icepack.interpolate(rasters['ex'], Q)
sigmaX = icepack.interpolate(firedrake.max_value(sigmaX, minSigma), Q)
sigmaX = icepack.interpolate(firedrake.min_value(sigmaX, maxSigma), Q)
sigmaY = icepack.interpolate(rasters['ey'], Q)
sigmaY = icepack.interpolate(firedrake.max_value(sigmaY, minSigma), Q)
sigmaY = icepack.interpolate(firedrake.min_value(sigmaY, maxSigma), Q)
speed = icepack.interpolate(firedrake.sqrt(inner(uObs, uObs)), Q)
# return results
return uObs, speed, sigmaX, sigmaY
def tracer_slice(tmpdir, degree):
n = 30 if degree == 0 else 15
m = PeriodicIntervalMesh(n, 1.)
mesh = ExtrudedMesh(m, layers=n, layer_height=1. / n)
# Parameters chosen so that dt != 1 and u != 1
# Gaussian is translated by 1.5 times width of domain to demonstrate
# that transport is working correctly
dt = 0.01
tmax = 0.75
output = OutputParameters(dirname=str(tmpdir), dumpfreq=25)
state = State(mesh, dt=dt, output=output)
uexpr = as_vector([2.0, 0.0])
x = SpatialCoordinate(mesh)
width = 1. / 10.
f0 = 0.5
fmax = 2.0
xc_init = 0.25
xc_end = 0.75
r_init = sqrt((x[0] - xc_init)**2 + (x[1] - 0.5)**2)
r_end = sqrt((x[0] - xc_end)**2 + (x[1] - 0.5)**2)
f_init = f0 + (fmax - f0) * exp(-(r_init / width)**2)
f_end = f0 + (fmax - f0) * exp(-(r_end / width)**2)
tol = 0.12
return TracerSetup(state,
tmax,
f_init,
f_end,
"CG",
degree,
uexpr,
tol=tol)
def min(f_in):
fmin = op2.Global(1, [np.finfo(float).max], dtype=float)
if len(f_in.ufl_shape) > 0:
mesh = f_in.function_space().mesh()
V = FunctionSpace(mesh, "DG", 1)
f = Function(V).project(sqrt(inner(f_in, f_in)))
else:
f = f_in
op2.par_loop(
op2.Kernel(
"""void minify(double *a, double *b)
{
a[0] = a[0] > fabs(b[0]) ? fabs(b[0]) : a[0];
}""", "minify"), f.dof_dset.set, fmin(op2.MIN), f.dat(op2.READ))
return fmin.data[0]
def compute(self, state):
u = state.field_dict['u']
dt = Constant(state.timestepping.dt)
return self.field(state.mesh).project(sqrt(dot(u, u))/sqrt(self.area(state.mesh))*dt)
def l2(f):
return sqrt(assemble(dot(f, f)*dx))