def _create_ode_solver(self):
"""Helper function to initialize a suitable ODE solver from
the cardiac model."""
# Extract cardiac cell model from cardiac model
cell_model = self._model.cell_models()
# Extract stimulus from the cardiac model(!)
if self.parameters['apply_stimulus_current_to_pde']:
stimulus = None
else:
stimulus = self._model.stimulus()
# Extract ode solver parameters
params = self.parameters["BasicCardiacODESolver"]
# Propagate enable_adjoint to Bidomain solver
if params.has_parameter("enable_adjoint"):
params["enable_adjoint"] = self.parameters["enable_adjoint"]
solver = BasicCardiacODESolver(self._heart_mesh,
self._time,
cell_model,
I_s=stimulus,
params=params)
return solver
def default_parameters():
"""Initialize and return a set of default parameters for the
splitting solver
*Returns*
A set of parameters (:py:class:`dolfin.Parameters`)
To inspect all the default parameters, do::
info(BasicSplittingSolver.default_parameters(), True)
"""
params = Parameters("BasicSplittingSolver")
params.add("enable_adjoint", True)
params.add("theta", 0.5, 0., 1.)
params.add("apply_stimulus_current_to_pde", False)
try:
params.add("pde_solver", "bidomain", set(["bidomain"]))
except:
params.add("pde_solver", "bidomain", ["bidomain"])
pass
# Add default parameters from ODE solver, but update for V
# space
ode_solver_params = BasicCardiacODESolver.default_parameters()
ode_solver_params["V_polynomial_degree"] = 1
ode_solver_params["V_polynomial_family"] = "CG"
params.add(ode_solver_params)
pde_solver_params = BasicBidomainSolver.default_parameters()
pde_solver_params["polynomial_degree"] = 1
params.add(pde_solver_params)
return params
def default_parameters():
"""Initialize and return a set of default parameters for the
splitting solver
*Returns*
The set of default parameters (:py:class:`dolfin.Parameters`)
*Example of usage*::
info(SplittingSolver.default_parameters(), True)
"""
params = Parameters("SplittingSolver")
params.add("enable_adjoint", True)
params.add("theta", 0.5, 0, 1)
params.add("apply_stimulus_current_to_pde", False)
try:
params.add("pde_solver", "bidomain",
set(["bidomain", "monodomain"]))
params.add("ode_solver_choice", "CardiacODESolver",
set(["BasicCardiacODESolver", "CardiacODESolver"]))
except:
params.add("pde_solver", "bidomain", ["bidomain", "monodomain"])
params.add("ode_solver_choice", "CardiacODESolver",
["BasicCardiacODESolver", "CardiacODESolver"])
pass
# Add default parameters from ODE solver
ode_solver_params = CardiacODESolver.default_parameters()
ode_solver_params["scheme"] = "RL1"
params.add(ode_solver_params)
# Add default parameters from ODE solver
basic_ode_solver_params = BasicCardiacODESolver.default_parameters()
basic_ode_solver_params["V_polynomial_degree"] = 1
basic_ode_solver_params["V_polynomial_family"] = "CG"
params.add(basic_ode_solver_params)
pde_solver_params = BidomainSolver.default_parameters()
pde_solver_params["polynomial_degree"] = 1
params.add(pde_solver_params)
pde_solver_params = MonodomainSolver.default_parameters()
pde_solver_params["polynomial_degree"] = 1
params.add(pde_solver_params)
return params