def passive(params):
logger.info(Text.blue("\nTest Passive Optimization"))
logger.info(pformat(params.to_dict()))
params["phase"] = "passive_inflation"
measurements, solver_parameters, p_lv, paramvec \
= setup_simulation(params, patient)
solver_parameters["relax_adjoint_solver"] = False
rd, paramvec = run_passive_optimization_step(params, patient,
solver_parameters,
measurements, p_lv, paramvec)
# Dump html visualization of the forward and adjoint system
adj_html("passive_forward.html", "forward")
adj_html("passive_adjoint.html", "adjoint")
# Replay the forward run, i.e make sure that the recording is correct.
logger.info("Replay dolfin")
assert replay_dolfin(tol=1e-12)
# Test that the gradient is correct
logger.info("Taylor test")
my_taylor_test(rd, paramvec)
paramvec_arr = gather_broadcast(paramvec.vector().array())
rd(paramvec_arr)
rd.for_res["initial_control"] = rd.initial_paramvec,
rd.for_res["optimal_control"] = rd.paramvec
store_results(params, rd, {})
def active(params):
logger.info(Text.blue("\nTest Passive Optimization"))
logger.info(pformat(params.to_dict()))
params["phase"] = "passive_inflation"
params["optimize_matparams"] = False
# patient.passive_filling_duration = 1
run_passive_optimization(params, patient)
adj_reset()
logger.info(Text.blue("\nTest Active Optimization"))
print(params["sim_file"])
params["phase"] = "active_contraction"
params["active_contraction_iteration_number"] = 0
measurements, solver_parameters, p_lv, gamma \
= setup_simulation(params, patient)
solver_parameters["relax_adjoint_solver"] = False
dolfin.parameters["adjoint"]["test_derivative"] = True
logger.info("Replay dolfin1")
replay_dolfin(tol=1e-12)
rd, gamma = run_active_optimization_step(params, patient,
solver_parameters, measurements,
p_lv, gamma)
# Dump html visualization of the forward and adjoint system
adj_html("active_forward.html", "forward")
adj_html("active_adjoint.html", "adjoint")
# Replay the forward run, i.e make sure that the recording is correct.
logger.info("Replay dolfin")
assert replay_dolfin(tol=1e-12)
# Test that the gradient is correct
logger.info("Taylor test")
my_taylor_test(rd, gamma)
paramvec_arr = gather_broadcast(gamma.vector().array())
rd(paramvec_arr)
rd.for_res["initial_control"] = rd.initial_paramvec,
rd.for_res["optimal_control"] = rd.paramvec
store_results(params, rd, {})
def test_iterate_gamma(problem):
target_gamma = 0.1
gamma = problem.material.activation
if has_dolfin_adjoint:
dolfin.parameters["adjoint"]["stop_annotating"] = False
dolfin_adjoint.adj_reset()
iterate(problem, gamma, target_gamma)
assert all(gamma.vector().get_local() == target_gamma)
assert dolfin.norm(problem.state.vector()) > 0
if has_dolfin_adjoint:
assert dolfin_adjoint.replay_dolfin(tol=1e-12)
def test_iterate_pressure(problem):
target_pressure = 1.0
plv = [p.traction for p in problem.bcs.neumann if p.name == 'lv']
pressure = plv[0]
if has_dolfin_adjoint:
dolfin.parameters["adjoint"]["stop_annotating"] = False
dolfin_adjoint.adj_reset()
iterate(problem, pressure, target_pressure)
if has_dolfin_adjoint:
# Check the recording
assert dolfin_adjoint.replay_dolfin(tol=1e-12)
# Check that the pressure is correct
assert float(plv[0]) == target_pressure
# Check that the state is nonzero
assert dolfin.norm(problem.state.vector()) > 0
def test_iterate_gamma_pressure(problem):
target_pressure = 1.0
plv = [p.traction for p in problem.bcs.neumann if p.name == 'lv']
pressure = plv[0]
target_gamma = 0.1
gamma = problem.material.activation
if has_dolfin_adjoint:
dolfin.parameters["adjoint"]["stop_annotating"] = False
dolfin_adjoint.adj_reset()
iterate(problem, (pressure, gamma), (target_pressure, target_gamma))
assert all(gamma.vector().get_local() == target_gamma)
assert float(plv[0]) == target_pressure
assert dolfin.norm(problem.state.vector()) > 0
if has_dolfin_adjoint:
assert dolfin_adjoint.replay_dolfin(tol=1e-12)
def test_iterate_gamma_cg1(continuation):
problem = make_lv_mechanics_problem('CG_1')
V = problem.material.activation.function_space()
target_gamma \
= dolfin.interpolate(dolfin.Expression('0.1 * x[0]',
degree=1), V)
gamma = problem.material.activation
if has_dolfin_adjoint:
dolfin.parameters["adjoint"]["stop_annotating"] = False
dolfin_adjoint.adj_reset()
iterate(problem, gamma, target_gamma, continuation=continuation)
assert np.all(
gamma.vector().get_local() - target_gamma.vector().get_local() < 1e-12)
assert dolfin.norm(problem.state.vector()) > 0
if has_dolfin_adjoint:
assert dolfin_adjoint.replay_dolfin(tol=1e-12)
def test_iterate_gamma_regional():
problem = make_lv_mechanics_problem('regional')
target_gamma = problem.material.activation.vector().get_local()
for i in range(len(target_gamma)):
target_gamma[i] = 0.1 - i * 0.001
print(target_gamma)
gamma = problem.material.activation
if has_dolfin_adjoint:
dolfin.parameters["adjoint"]["stop_annotating"] = False
dolfin_adjoint.adj_reset()
iterate(problem, gamma, target_gamma)
print(gamma.vector().get_local())
assert np.all(gamma.vector().get_local() - target_gamma < 1e-12)
assert dolfin.norm(problem.state.vector()) > 0
if has_dolfin_adjoint:
assert dolfin_adjoint.replay_dolfin(tol=1e-12)
model = ReducedFunctional(config, scale = -1)
m0 = model.initial_control()
# Build the turbine cache
config.turbine_cache.update(config)
time_forward = []
time_adjoint = []
for i in range(5):
print "Running forward model round ", i
t1 = Timer("Forward model")
model.run_forward_model_mem.fn(m0)
time_forward.append(t1.stop())
print "Forward model runtime: ", time_forward[-1]
from dolfin_adjoint import replay_dolfin
print "Replaying model round ", i
t11 = Timer("Replay forward model")
replay_dolfin()
print "Replay model runtime: ", t11.stop()
t2 = Timer("Adjoint model")
model.run_adjoint_model_mem.fn(m0)
time_adjoint.append(t2.stop())
print "Adjoint model runtime: ", time_adjoint[-1]
print "Smallest runtime for forward model: ", min(time_forward)
print "Smallest runtime for forward + adjoint model: ", min(time_forward) + min(time_adjoint)
print "Ratio: ", 1.0 + min(time_adjoint) / min(time_forward)
model = ReducedFunctional(config, scale=-1, plot=True)
m0 = model.initial_control()
# Build the turbine cache
config.turbine_cache.update(config)
time_forward = []
time_adjoint = []
for i in range(5):
print "Running forward model round ", i
t1 = Timer("Forward model")
model.run_forward_model_mem.fn(m0)
time_forward.append(t1.stop())
print "Forward model runtime: ", time_forward[-1]
from dolfin_adjoint import replay_dolfin
print "Replaying model round ", i
t11 = Timer("Replay forward model")
replay_dolfin()
print "Replay model runtime: ", t11.stop()
t2 = Timer("Adjoint model")
model.run_adjoint_model_mem.fn(m0)
time_adjoint.append(t2.stop())
print "Adjoint model runtime: ", time_adjoint[-1]
print "Smallest runtime for forward model: ", min(time_forward)
print "Smallest runtime for forward + adjoint model: ", min(
time_forward) + min(time_adjoint)
print "Ratio: ", 1.0 + min(time_adjoint) / min(time_forward)
