def test_add_field():
pp = PostProcessor()
pp.add_field(SolutionField("foo"))
assert "foo" in pp._fields.keys()
pp += SolutionField("bar")
assert set(["foo", "bar"]) == set(pp._fields.keys())
pp += [SolutionField("a"), SolutionField("b")]
assert set(["foo", "bar", "a", "b"]) == set(pp._fields.keys())
pp.add_fields([
MetaField("foo"),
MetaField2("foo", "bar"),
])
assert set(["foo", "bar", "a", "b", "MetaField_foo",
"MetaField2_foo_bar"]) == set(pp._fields.keys())
def test_update_all():
pressure = SolutionField("MockPressure") #MockPressure()
velocity = SolutionField("MockVelocity") #MockVelocity()
Du = MockVelocityGradient()
epsilon = MockStrain(dict(start_timestep=3))
sigma = MockStress(dict(start_time=0.5, end_time=0.8))
# Add fields to postprocessor
pp = PostProcessor()
pp.add_fields([pressure, velocity, Du, epsilon, sigma])
N = 11
T = [(i, float(i) / (N - 1)) for i in xrange(N)]
for timestep, t in T:
pp.update_all(
{
"MockPressure": lambda: "p" + str(timestep),
"MockVelocity": lambda: "u" + str(timestep)
}, t, timestep)
assert Du.touched == timestep + 1
assert pp._cache[0]["MockPressure"] == "p%d" % timestep
assert pp._cache[0]["MockVelocity"] == "u%d" % timestep
assert pp._cache[0]["MockVelocityGradient"] == "grad(u%d)" % timestep
if timestep >= 3:
assert pp._cache[0][
"MockStrain"] == "epsilon(grad(u%d))" % timestep
else:
assert "MockStrain" not in pp._cache[0]
if 0.5 <= t <= 0.8:
assert pp._cache[0][
"MockStress"] == "sigma(epsilon(grad(u%d)), p%d)" % (timestep,
timestep)
else:
assert "MockStress" not in pp._cache[0]
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "KinematicViscosity", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "FluidDensity", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "FluidDensity", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "Pressure", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "Pressure", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "Velocity", params, label)
def __init__(self, params=None, label=None):
SolutionField.__init__(self, "Velocity", params, label)
def run_splitting_solver(domain, dt, T):
# Create cardiac model problem description
cell_model = Tentusscher_panfilov_2006_epi_cell()
heart = setup_model(cell_model, domain)
# Customize and create monodomain solver
ps = SplittingSolver.default_parameters()
ps["pde_solver"] = "monodomain"
ps["apply_stimulus_current_to_pde"] = True
# 2nd order splitting scheme
ps["theta"] = 0.5
# Use explicit first-order Rush-Larsen scheme for the ODEs
ps["ode_solver_choice"] = "CardiacODESolver"
ps["CardiacODESolver"]["scheme"] = "RL1"
# Crank-Nicolson discretization for PDEs in time:
ps["MonodomainSolver"]["theta"] = 0.5
ps["MonodomainSolver"]["linear_solver_type"] = "iterative"
ps["MonodomainSolver"]["algorithm"] = "cg"
ps["MonodomainSolver"]["preconditioner"] = "petsc_amg"
# Create solver
solver = SplittingSolver(heart, params=ps)
# Extract the solution fields and set the initial conditions
(vs_, vs, vur) = solver.solution_fields()
vs_.assign(cell_model.initial_conditions())
solutions = solver.solve((0, T), dt)
postprocessor = PostProcessor(dict(casedir="test", clean_casedir=True))
postprocessor.store_mesh(heart.domain())
field_params = dict(
save=True,
save_as=["hdf5", "xdmf"],
plot=False,
start_timestep=-1,
stride_timestep=1
)
postprocessor.add_field(SolutionField("v", field_params))
theta = ps["theta"]
# Solve
total = Timer("XXX Total cbcbeat solver time")
for i, (timestep, (vs_, vs, vur)) in enumerate(solutions):
t0, t1 = timestep
current_t = t0 + theta*(t1 - t0)
postprocessor.update_all({"v": lambda: vur}, current_t, i)
print("Solving on %s" % str(timestep))
# Print memory usage (just for the fun of it)
print(memory_usage())
total.stop()
# Plot result (as sanity check)
#plot(vs[0], interactive=True)
# Stop timer and list timings
if MPI.rank(mpi_comm_world()) == 0:
list_timings(TimingClear_keep, [TimingType_wall])