def setup(self):
self.mesh = UnitCubeMesh(5, 5, 5)
# Create time
self.time = Constant(0.0)
# Create stimulus
self.stimulus = Expression("2.0*t", t=self.time, degree=1)
# Create ac
self.applied_current = Expression("sin(2*pi*x[0])*t",
t=self.time,
degree=3)
# Create conductivity "tensors"
self.M_i = 1.0
self.M_e = 2.0
self.cell_model = FitzHughNagumoManual()
self.cardiac_model = CardiacModel(self.mesh, self.time, self.M_i,
self.M_e, self.cell_model,
self.stimulus, self.applied_current)
dt = 0.1
self.t0 = 0.0
self.dt = [(0.0, dt), (dt * 2, dt / 2), (dt * 4, dt)]
# Test using variable dt interval but using the same dt.
self.T = self.t0 + 5 * dt
self.ics = self.cell_model.initial_conditions()
def __init__(self):
self.mesh = UnitCubeMesh(5, 5, 5)
# Create time
self.time = Constant(0.0)
# Create stimulus
self.stimulus = Expression("2.0*t", t=self.time, degree=1)
# Create ac
self.applied_current = Expression("sin(2*pi*x[0])*t",
t=self.time,
degree=3)
# Create conductivity "tensors"
self.M_i = 1.0
self.M_e = 2.0
self.cell_model = FitzHughNagumoManual()
self.cardiac_model = CardiacModel(self.mesh, self.time, self.M_i,
self.M_e, self.cell_model,
self.stimulus,
self.applied_current)
dt = 0.1
self.t0 = 0.0
if Solver == SplittingSolver:
# FIXME: Dolfin-adjoint fails with adaptive timestep and SplittingSolver
self.dt = dt
else:
self.dt = [(0.0, dt), (dt * 2, dt / 2), (dt * 4, dt)]
# Test using variable dt interval but using the same dt.
self.T = self.t0 + 5 * dt
# Create solver object
params = Solver.default_parameters()
if Solver == SplittingSolver:
params.enable_adjoint = enable_adjoint
params.BidomainSolver.linear_solver_type = solver_type
params.BidomainSolver.petsc_krylov_solver.relative_tolerance = 1e-12
else:
params.BasicBidomainSolver.linear_variational_solver.linear_solver = \
"gmres" if solver_type == "iterative" else "lu"
params.BasicBidomainSolver.linear_variational_solver.krylov_solver.relative_tolerance = 1e-12
params.BasicBidomainSolver.linear_variational_solver.preconditioner = 'ilu'
self.solver = Solver(self.cardiac_model, params=params)
(vs_, vs, vur) = self.solver.solution_fields()
if ics is None:
self.ics = self.cell_model.initial_conditions()
vs_.assign(self.ics)
else:
vs_.vector()[:] = ics.vector()
def setup(self):
self.mesh = UnitCubeMesh(5, 5, 5)
self.time = Constant(0.0)
# Create stimulus
self.stimulus = Expression("2.0", degree=1)
# Create applied current
self.applied_current = Expression("sin(2*pi*x[0])*t", t=self.time,
degree=3)
# Create conductivity "tensors"
self.M_i = 1.0
self.M_e = 2.0
self.t0 = 0.0
self.dt = 0.1
self.T = 5*self.dt
def test_solver_with_domains():
mesh = UnitCubeMesh(5, 5, 5)
time = Constant(0.0)
stimulus = Expression("2.0*t", t=time, degree=1)
# Create ac
applied_current = Expression("sin(2*pi*x[0])*t", t=time, degree=3)
# Create conductivity "tensors"
M_i = 1.0
M_e = 2.0
cell_model = FitzHughNagumoManual()
cardiac_model = CardiacModel(mesh, time, M_i, M_e, cell_model,
stimulus, applied_current)
dt = 0.1
t0 = 0.0
dt = dt
T = t0 + 5*dt
ics = cell_model.initial_conditions()
# Create basic solver
params = SplittingSolver.default_parameters()
params["ode_solver_choice"] = "BasicCardiacODESolver"
solver = SplittingSolver(cardiac_model, params=params)
(vs_, vs, vur) = solver.solution_fields()
vs_.assign(ics)
# Solve
solutions = solver.solve((t0, T), dt)
for (interval, fields) in solutions:
(vs_, vs, vur) = fields
def setup(self):
self.mesh = UnitCubeMesh(2, 2, 2)
self.cell_model = FitzHughNagumoManual()
self.cardiac_model = CardiacModel(self.mesh, None,
1.0, 2.0,
self.cell_model)