def solve(self, var, b):
x = dolfin.Function(self.test_function().function_space())
# b is a libadjoint object (form or function)
(a, L) = (self.data, b.data)
# First: check if L is None (meaning zero)
if L is None:
x_vec = adjlinalg.Vector(x)
return x_vec
if isinstance(L, dolfin.Function):
b_vec = L.vector()
L = None
else:
b_vec = dolfin.assemble(L)
# Next: if necessary, create a new solver and add to dictionary
idx = a.arguments()
if idx not in caching.localsolvers:
if dolfin.parameters["adjoint"]["debug_cache"]:
dolfin.info_red("Creating new LocalSolver")
newsolver = dolfin.LocalSolver(a, None, solver_type=self.solver_parameters["solver_type"])
if self.solver_parameters["factorize"] : newsolver.factorize()
caching.localsolvers[idx] = newsolver
else:
if dolfin.parameters["adjoint"]["debug_cache"]:
dolfin.info_green("Reusing LocalSolver")
# Get the right solver from the solver dictionary
solver = caching.localsolvers[idx]
solver.solve_local(x.vector(), b_vec, b.fn_space.dofmap())
x_vec = adjlinalg.Vector(x)
return x_vec
def _setup_solver(self, Model, Scheme, time=0.0, stim=None, params=None):
''' Generate a new solver object with the given start time, stimulus and parameters. '''
# Create model instance
if isinstance(Model, str):
Model = eval(Model)
model = Model(params=params)
# Initialize time and stimulus (note t=time construction!)
if stim is None:
stim = Expression("1000*t", t=time, degree=1)
# Initialize solver
mesh = UnitIntervalMesh(5)
params = CardiacODESolver.default_parameters()
params["scheme"] = Scheme
solver = CardiacODESolver(mesh, time, model, I_s=stim, params=params)
# Create scheme
info_green("\nTesting %s with %s scheme" % (model, Scheme))
# Start with native initial conditions
(vs_, vs) = solver.solution_fields()
vs_.assign(model.initial_conditions())
vs.assign(vs_)
return solver
def test_default_basic_single_cell_solver(self, cell_model, theta):
"Test basic single cell solver."
time = Constant(0.0)
model = cell_model
Model = cell_model.__class__
if Model == supported_cell_models[3] and theta > 0:
pytest.xfail("failing configuration (but should work)")
model.stimulus = Expression("1000*t", t=time, degree=1)
info_green("\nTesting %s" % model)
vec_solve = self._run_solve(model, time, theta)
if Model == supported_cell_models[3] and theta == 0:
pytest.xfail("failing configuration (but should work)")
if Model in self.references and theta in self.references[Model]:
ind, ref_value = self.references[Model][theta]
print("vec_solve", vec_solve.array())
print("ind", ind, "ref", ref_value)
assert_almost_equal(vec_solve[ind], ref_value, 1e-10)
else:
info_red("Missing references for %r, %r" % (Model, theta))
def test_ReplayOfSplittingSolver_IsExact(self, Solver, solver_type, tol):
"""Test that basic and optimised splitting solvers yield
very comparative results when configured identically."""
self.tlm_adj_setup(Solver, solver_type)
info_green("Replaying")
success = replay_dolfin(tol=tol, stop=True)
assert success
def test_AdjointModelOfSplittingSolver_PassesTaylorTest(
self, Solver, solver_type):
"""Test that basic and optimised splitting solvers yield
very comparative results when configured identically."""
J, Jhat, m, Jics = self.tlm_adj_setup(Solver, solver_type)
# Check adjoint model correctness
info_green("Compute gradient with adjoint linear model")
dJdics = compute_gradient(J, m, forget=False)
assert (dJdics is not None), "Gradient is None (#fail)."
conv_rate = taylor_test(Jhat, m, Jics, dJdics, seed=1.)
# Check that minimal convergence rate is greater than some given number
assert_greater(conv_rate, 1.9)
def test_TangentLinearModelOfSplittingSolver_PassesTaylorTest(
self, Solver, solver_type):
"""Test that basic and optimised splitting solvers yield
very comparative results when configured identically."""
if isinstance(Solver, BasicSplittingSolver):
pytest.mark.xfail("PETSc error 73: Object is in wring state")
J, Jhat, m, Jics = self.tlm_adj_setup(Solver, solver_type)
# Check TLM correctness
info_green("Compute gradient with tangent linear model")
dJdics = compute_gradient_tlm(J, m, forget=False)
assert (dJdics is not None), "Gradient is None (#fail)."
conv_rate_tlm = taylor_test(Jhat, m, Jics, dJdics, seed=1)
# Check that minimal convergence rate is greater than some given number
assert_greater(conv_rate_tlm, 1.9)
def _setup_solver(self, Model, Scheme, mesh, time, stim=None, params=None):
# Create model instance
model = Model(params=params)
# Initialize time and stimulus (note t=time construction!)
if stim is None:
stim = Expression("1000*t", t=time, degree=1)
# Initialize solver
params = CardiacODESolver.default_parameters()
params["scheme"] = Scheme
solver = CardiacODESolver(mesh, time, model, I_s=stim, params=params)
# Create scheme
info_green("\nTesting %s with %s scheme" % (model, Scheme))
# Start with native initial conditions
(vs_, vs) = solver.solution_fields()
vs_.assign(model.initial_conditions())
vs.assign(vs_)
return solver
def solve(self, var, b):
x = dolfin.Function(self.test_function().function_space())
# b is a libadjoint object (form or function)
(a, L) = (self.data, b.data)
# First: check if L is None (meaning zero)
if L is None:
x_vec = adjlinalg.Vector(x)
return x_vec
if isinstance(L, dolfin.Function):
b_vec = L.vector()
L = None
else:
b_vec = dolfin.assemble(L)
# Next: if necessary, create a new solver and add to dictionary
idx = a.arguments()
if idx not in caching.localsolvers:
if dolfin.parameters["adjoint"]["debug_cache"]:
dolfin.info_red("Creating new LocalSolver")
newsolver = dolfin.LocalSolver(
a, None, solver_type=self.solver_parameters["solver_type"])
if self.solver_parameters["factorize"]: newsolver.factorize()
caching.localsolvers[idx] = newsolver
else:
if dolfin.parameters["adjoint"]["debug_cache"]:
dolfin.info_green("Reusing LocalSolver")
# Get the right solver from the solver dictionary
solver = caching.localsolvers[idx]
solver.solve_local(x.vector(), b_vec, b.fn_space.dofmap())
x_vec = adjlinalg.Vector(x)
return x_vec
def info_green(self, message, values, log_keys, time=None):
info_green(message % values)
self._log_data(values, log_keys, time)
def __init__(self, turbine, flow):
# add radius to model params
if model_parameters is None:
model_parameters = {"radius": turbine_radius}
else:
model_parameters.update({"radius": turbine_radius})
# check if gradient required
if "compute_gradient" in model_parameters:
compute_gradient = model_parameters["compute_gradient"]
else:
compute_gradient = True
# check if a wake and wake gradients are provided
if "wake" in model_parameters:
if "wake_gradients" in model_parameters:
gradients = model_parameters["wake_gradients"]
else:
gradients = None
self.wake = ADDolfinExpression(model_parameters["wake"],
compute_gradient=compute_gradient,
gradients=gradients)
# compute wake and gradients
else:
# mimic a SteadyConfiguration but change a few things along the way
config = otf.DefaultConfiguration()
config.params['steady_state'] = True
config.params[
'initial_condition'] = otf.ConstantFlowInitialCondition(config)
config.params['include_advection'] = True
config.params['include_diffusion'] = True
config.params['diffusion_coef'] = 3.0
config.params['quadratic_friction'] = True
config.params['newton_solver'] = True
config.params['friction'] = dolfin.Constant(0.0025)
config.params['theta'] = 1.0
config.params["dump_period"] = 0
xmin, ymin = -100, -200
xsize, ysize = 1000, 400
xcells, ycells = 400, 160
mesh = dolfin.RectangleMesh(xmin, ymin, xmin + xsize, ymin + ysize,
xcells, ycells)
V, H = config.finite_element(mesh)
config.function_space = dolfin.MixedFunctionSpace([V, H])
config.turbine_function_space = dolfin.FunctionSpace(mesh, 'CG', 2)
class Domain(object):
"""
Domain object used for setting boundary conditions etc later on
"""
def __init__(self, mesh):
class InFlow(dolfin.SubDomain):
def inside(self, x, on_boundary):
return dolfin.near(x[0], -100)
class OutFlow(dolfin.SubDomain):
def inside(self, x, on_boundary):
return dolfin.near(x[0], 900)
inflow = InFlow()
outflow = OutFlow()
self.mesh = mesh
self.boundaries = dolfin.FacetFunction("size_t", mesh)
self.boundaries.set_all(0)
inflow.mark(self.boundaries, 1)
outflow.mark(self.boundaries, 2)
self.ds = dolfin.Measure('ds')[self.boundaries]
config.domain = Domain(mesh)
config.set_domain(config.domain, warning=False)
# Boundary conditions
bc = otf.DirichletBCSet(config)
bc.add_constant_flow(1, 1.0 + 1e-10)
bc.add_zero_eta(2)
config.params['bctype'] = 'strong_dirichlet'
config.params['strong_bc'] = bc
config.params['free_slip_on_sides'] = True
# Optimisation settings
config.params['functional_final_time_only'] = True
config.params['automatic_scaling'] = False
# Turbine settings
config.params['turbine_pos'] = []
config.params['turbine_friction'] = []
config.params['turbine_x'] = turbine_radius * 2
config.params['turbine_y'] = turbine_radius * 2
config.params['controls'] = ['turbine_pos']
# Finally set some DOLFIN optimisation flags
dolfin.parameters['form_compiler']['cpp_optimize'] = True
dolfin.parameters['form_compiler']['cpp_optimize_flags'] = '-O3'
dolfin.parameters['form_compiler']['optimize'] = True
# place a turbine with default friction
turbine = [(0., 0.)]
config.set_turbine_pos(turbine)
# solve the shallow water equations
rf = otf.ReducedFunctional(config, plot=False)
dolfin.info_blue("Generating the wake model...")
rf.j(rf.initial_control())
# get state
state = rf.last_state
V = dolfin.VectorFunctionSpace(config.function_space.mesh(),
"CG",
2,
dim=2)
u_out = dolfin.TrialFunction(V)
v_out = dolfin.TestFunction(V)
M_out = dolfin_adjoint.assemble(
dolfin.inner(v_out, u_out) * dolfin.dx)
out_state = dolfin.Function(V)
rhs = dolfin_adjoint.assemble(
dolfin.inner(v_out,
state.split()[0]) * dolfin.dx)
dolfin_adjoint.solve(M_out,
out_state.vector(),
rhs,
"cg",
"sor",
annotate=False)
dolfin.info_green("Wake model generated.")
self.wake = ADDolfinExpression(out_state.split()[0],
compute_gradient)
super(ApproximateShallowWater,
self).__init__("ApproximateShallowWater", flow_field,
model_parameters)
def info_green(*args, **kwargs):
if MPI.process_number() == 0:
dolfin.info_green(*args, **kwargs)
def info_green(*args, **kwargs):
if MPI.process_number() == 0:
dolfin.info_green(*args, **kwargs)
def info_green(*args, **kwargs):
if get_rank() == 0:
dolfin.info_green(*args, **kwargs)
def mg_opt(rf, meshes, current_mesh_idx):
if current_mesh_idx == len(meshes) - 1:
info_green("Solve problem on coarsest grid")
m_h_p1 = minimize(rf)
else:
m_h1 = minimize(rf, options = {"maxiter": 1})
def mg_opt(rf, meshes, current_mesh_idx):
if current_mesh_idx == len(meshes) - 1:
info_green("Solve problem on coarsest grid")
m_h_p1 = minimize(rf)
else:
m_h1 = minimize(rf, options = {"maxiter": 1})