def normalise_eigen(self, v, beta, mode='none'):
if mode == 'none':
return
elif mode == 'one':
coef = beta.vector().norm('l2')
elif mode == 'max':
coef = max(abs(beta.vector()[:]))
coeff_glob = np.array(0.0, 'd')
comm.Allreduce(coef, coeff_glob, op=mpi4py.MPI.MAX)
log(LogLevel.DEBUG, 'Normalising eigenvector mode={}'.format(mode))
real = np.all(np.isfinite(v.vector()[:]))
log(LogLevel.DEBUG, '{}: v vector real {}'.format(rank, real))
real = np.all(np.isfinite(beta.vector()[:]))
log(LogLevel.DEBUG, '{}: beta vector real {}'.format(rank, real))
log(LogLevel.DEBUG, '{}: coeff {}'.format(rank, coef))
log(LogLevel.DEBUG, '{}: coeff_glob {}'.format(rank, coeff_glob))
vval = v.vector()[:] / coeff_glob
bval = beta.vector()[:] / coeff_glob
v.vector().set_local(vval)
beta.vector().set_local(bval)
v.vector().vec().ghostUpdate()
beta.vector().vec().ghostUpdate()
return coeff_glob
def test_reduced_mesh_load_collapsed_matrix(mesh, load_tempdir):
log(PROGRESS, "*** Collapsed case, matrix, online computation ***")
(V, U) = CollapsedFunctionSpaces(mesh)
reduced_mesh = ReducedMesh((V, U))
reduced_mesh.load(load_tempdir, "test_reduced_mesh_collapsed_matrix")
_test_reduced_mesh_collapsed_matrix(V, U, reduced_mesh)
def update_lower_bound(self):
"""
Update lower bound.
"""
alpha = self.state["alpha"]
self.lb = alpha.copy(deepcopy=True).vector()
log(LogLevel.DEBUG, 'DEBUG: Updated irreversibility')
def _test_reduced_mesh_elliptic_function(V, reduced_mesh):
reduced_V = reduced_mesh.get_reduced_function_spaces()
dofs = [d[0] for d in reduced_mesh.get_dofs_list()] # convert from 1-tuple to int
reduced_dofs = [d[0] for d in reduced_mesh.get_reduced_dofs_list()] # convert from 1-tuple to int
mesh_dim = V.mesh().geometry().dim()
assert mesh_dim in (1, 2)
if mesh_dim is 1:
e = Expression("1+x[0]", element=V.ufl_element())
else:
e = Expression("(1+x[0])*(1+x[1])", element=V.ufl_element())
f = project(e, V)
f_N = project(e, reduced_V[0])
f_dofs = evaluate_sparse_function_at_dofs(f, dofs, V, dofs)
f_reduced_dofs = evaluate_sparse_function_at_dofs(f, dofs, reduced_V[0], reduced_dofs)
f_N_reduced_dofs = evaluate_sparse_function_at_dofs(f_N, reduced_dofs, reduced_V[0], reduced_dofs)
log(PROGRESS, "f at dofs:\n" + str(nonzero_values(f_dofs)))
log(PROGRESS, "f at reduced dofs:\n" + str(nonzero_values(f_reduced_dofs)))
log(PROGRESS, "f_N at reduced dofs:\n" + str(nonzero_values(f_N_reduced_dofs)))
log(PROGRESS, "Error:\n" + str(nonzero_values(f_dofs) - nonzero_values(f_reduced_dofs)))
log(PROGRESS, "Error:\n" + str(f_reduced_dofs.vector().get_local() - f_N_reduced_dofs.vector().get_local()))
assert isclose(nonzero_values(f_dofs), nonzero_values(f_reduced_dofs)).all()
assert isclose(f_reduced_dofs.vector().get_local(), f_N_reduced_dofs.vector().get_local()).all()
def test_reduced_mesh_load_collapsed_vector(mesh, load_tempdir):
log(PROGRESS, "*** Collapsed case, vector, online computation ***")
(V, _) = CollapsedFunctionSpaces(mesh)
reduced_mesh = ReducedMesh((V, ))
reduced_mesh.load(load_tempdir, "test_reduced_mesh_collapsed_vector")
_test_reduced_mesh_collapsed_vector(V, reduced_mesh)
def test_separated_parametrized_forms_vector_6():
a6 = inner(expr7 * grad(u), grad(v)) * dx + inner(
grad(u) * expr6, v) * dx + expr5 * inner(u, v) * dx
a6_sep = SeparatedParametrizedForm(a6)
log(PROGRESS, "*** ### FORM 6 ### ***")
log(
PROGRESS,
"We change the coefficients to be non-parametrized. No (parametrized) coefficients are extracted this time"
)
a6_sep.separate()
log(
PROGRESS, "\tLen coefficients:\n" + "\t\t" +
str(len(a6_sep.coefficients)) + "\n")
assert 0 == len(a6_sep.coefficients)
log(
PROGRESS, "\tLen unchanged forms:\n" + "\t\t" +
str(len(a6_sep._form_unchanged)) + "\n")
assert 3 == len(a6_sep._form_unchanged)
log(
PROGRESS, "\tUnchanged forms:\n" + "\t\t" +
str(a6_sep._form_unchanged[0].integrals()[0].integrand()) + "\n" +
"\t\t" + str(a6_sep._form_unchanged[1].integrals()[0].integrand()) +
"\n" + "\t\t" +
str(a6_sep._form_unchanged[2].integrals()[0].integrand()) + "\n")
assert "sum_{i_{72}} sum_{i_{71}} ({ A | A_{i_{66}, i_{67}} = sum_{i_{68}} f_11[i_{66}, i_{68}] * (grad(v_1))[i_{68}, i_{67}] })[i_{71}, i_{72}] * (grad(v_0))[i_{71}, i_{72}] " == str(
a6_sep._form_unchanged[0].integrals()[0].integrand())
assert "sum_{i_{73}} ({ A | A_{i_{69}} = sum_{i_{70}} f_10[i_{70}] * (grad(v_1))[i_{69}, i_{70}] })[i_{73}] * v_0[i_{73}] " == str(
a6_sep._form_unchanged[1].integrals()[0].integrand())
assert "f_9 * (sum_{i_{74}} v_0[i_{74}] * v_1[i_{74}] )" == str(
a6_sep._form_unchanged[2].integrals()[0].integrand())
def test_separated_parametrized_forms_vector_18():
a18 = inner(grad(expr14[0]), u) * v[0] * dx + expr14[0].dx(0) * inner(
u, v) * dx
a18_sep = SeparatedParametrizedForm(a18)
log(PROGRESS, "*** ### FORM 18 ### ***")
log(
PROGRESS,
"This form is similar to form 14, but each term is multiplied by the gradient/partial derivative of a component of a Function which is not solution of a parametrized problem. This results in no parametrized coefficients"
)
a18_sep.separate()
log(
PROGRESS, "\tLen coefficients:\n" + "\t\t" +
str(len(a18_sep.coefficients)) + "\n")
assert 0 == len(a18_sep.coefficients)
log(
PROGRESS, "\tLen unchanged forms:\n" + "\t\t" +
str(len(a18_sep._form_unchanged)) + "\n")
assert 2 == len(a18_sep._form_unchanged)
log(
PROGRESS, "\tUnchanged forms:\n" + "\t\t" +
str(a18_sep._form_unchanged[0].integrals()[0].integrand()) + "\n" +
"\t\t" + str(a18_sep._form_unchanged[1].integrals()[0].integrand()) +
"\n")
assert "v_0[0] * (sum_{i_{177}} (grad(f_30))[0, i_{177}] * v_1[i_{177}] )" == str(
a18_sep._form_unchanged[0].integrals()[0].integrand())
assert "(grad(f_30))[0, 0] * (sum_{i_{178}} v_0[i_{178}] * v_1[i_{178}] )" == str(
a18_sep._form_unchanged[1].integrals()[0].integrand())
def test_separated_parametrized_forms_vector_13():
a13 = inner(expr15 * grad(u), grad(v)) * dx + inner(
grad(u) * expr14, v) * dx + expr13 * inner(u, v) * dx
a13_sep = SeparatedParametrizedForm(a13)
log(PROGRESS, "*** ### FORM 13 ### ***")
log(
PROGRESS,
"This form is similar to form 11, but each term is multiplied by a Function, which is not the solution of a parametrized problem. This results in no parametrized coefficients"
)
a13_sep.separate()
log(
PROGRESS, "\tLen coefficients:\n" + "\t\t" +
str(len(a13_sep.coefficients)) + "\n")
assert 0 == len(a13_sep.coefficients)
log(
PROGRESS, "\tLen unchanged forms:\n" + "\t\t" +
str(len(a13_sep._form_unchanged)) + "\n")
assert 3 == len(a13_sep._form_unchanged)
log(
PROGRESS, "\tUnchanged forms:\n" + "\t\t" +
str(a13_sep._form_unchanged[0].integrals()[0].integrand()) + "\n" +
"\t\t" + str(a13_sep._form_unchanged[1].integrals()[0].integrand()) +
"\n" + "\t\t" +
str(a13_sep._form_unchanged[2].integrals()[0].integrand()) + "\n")
assert "sum_{i_{151}} sum_{i_{150}} ({ A | A_{i_{145}, i_{146}} = sum_{i_{147}} f_33[i_{145}, i_{147}] * (grad(v_1))[i_{147}, i_{146}] })[i_{150}, i_{151}] * (grad(v_0))[i_{150}, i_{151}] " == str(
a13_sep._form_unchanged[0].integrals()[0].integrand())
assert "sum_{i_{152}} ({ A | A_{i_{148}} = sum_{i_{149}} f_30[i_{149}] * (grad(v_1))[i_{148}, i_{149}] })[i_{152}] * v_0[i_{152}] " == str(
a13_sep._form_unchanged[1].integrals()[0].integrand())
assert "f_27 * (sum_{i_{153}} v_0[i_{153}] * v_1[i_{153}] )" == str(
a13_sep._form_unchanged[2].integrals()[0].integrand())
def test_separated_parametrized_forms_vector_17():
a17 = inner(grad(expr14) * grad(u), grad(v)) * dx + inner(
grad(u) * grad(expr13), v) * dx + expr13.dx(0) * inner(u, v) * dx
a17_sep = SeparatedParametrizedForm(a17)
log(PROGRESS, "*** ### FORM 17 ### ***")
log(
PROGRESS,
"This form is similar to form 13, but each term is multiplied by a the gradient/partial derivative of Function, which is not the solution of a parametrized problem. This results in no parametrized coefficients"
)
a17_sep.separate()
log(
PROGRESS, "\tLen coefficients:\n" + "\t\t" +
str(len(a17_sep.coefficients)) + "\n")
assert 0 == len(a17_sep.coefficients)
log(
PROGRESS, "\tLen unchanged forms:\n" + "\t\t" +
str(len(a17_sep._form_unchanged)) + "\n")
assert 3 == len(a17_sep._form_unchanged)
log(
PROGRESS, "\tUnchanged forms:\n" + "\t\t" +
str(a17_sep._form_unchanged[0].integrals()[0].integrand()) + "\n" +
"\t\t" + str(a17_sep._form_unchanged[1].integrals()[0].integrand()) +
"\n" + "\t\t" +
str(a17_sep._form_unchanged[2].integrals()[0].integrand()) + "\n")
assert "sum_{i_{174}} sum_{i_{173}} ({ A | A_{i_{168}, i_{169}} = sum_{i_{170}} (grad(v_1))[i_{170}, i_{169}] * (grad(f_30))[i_{168}, i_{170}] })[i_{173}, i_{174}] * (grad(v_0))[i_{173}, i_{174}] " == str(
a17_sep._form_unchanged[0].integrals()[0].integrand())
assert "sum_{i_{175}} ({ A | A_{i_{171}} = sum_{i_{172}} (grad(v_1))[i_{171}, i_{172}] * (grad(f_27))[i_{172}] })[i_{175}] * v_0[i_{175}] " == str(
a17_sep._form_unchanged[1].integrals()[0].integrand())
assert "(grad(f_27))[0] * (sum_{i_{176}} v_0[i_{176}] * v_1[i_{176}] )" == str(
a17_sep._form_unchanged[2].integrals()[0].integrand())
def test_reduced_mesh_load_mixed_vector(mesh, load_tempdir):
log(PROGRESS, "*** Mixed case, vector, online computation ***")
V = MixedFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, ))
reduced_mesh.load(load_tempdir, "test_reduced_mesh_mixed_vector")
_test_reduced_mesh_mixed_vector(V, reduced_mesh)
def test_reduced_mesh_load_elliptic_matrix(mesh, load_tempdir):
log(PROGRESS, "*** Elliptic case, matrix, online computation ***")
V = EllipticFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, V))
reduced_mesh.load(load_tempdir, "test_reduced_mesh_elliptic_matrix")
_test_reduced_mesh_elliptic_matrix(V, reduced_mesh)
def test_reduced_mesh_load_elliptic_vector(mesh, load_tempdir):
log(PROGRESS, "*** Elliptic case, vector, online computation ***")
V = EllipticFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, ))
reduced_mesh.load(load_tempdir, "test_reduced_mesh_elliptic_vector")
_test_reduced_mesh_elliptic_vector(V, reduced_mesh)
def solve(self):
log(LogLevel.INFO,
'________________________ EQUILIBRIUM _________________________')
log(LogLevel.INFO, 'Solving elasticity')
problem = self.problem
u = problem.state["u"].vector()
self.solver.solve(problem, u)
return (self.solver.snes().getIterationNumber(),
self.solver.snes().getConvergedReason())
def plotstep():
if rank == 0:
fig = plt.figure(dpi=80, facecolor='w', edgecolor='k')
plt.subplot(1, 1, 1)
plt.set_cmap('binary')
dolfin.plot(
project(stability.inactivemarker4, L2), alpha = 1., vmin=0., vmax=1.)
plt.title('intersec deriv, ub')
plt.savefig(os.path.join(outdir, "inactivesets-{:.3f}-{:d}.pdf".format(load, iteration)))
plt.set_cmap('hot')
fig = plt.figure(dpi=80, facecolor='w', edgecolor='k')
for i,mode in enumerate(pert):
plt.subplot(2, _nmodes+1, i+2)
plt.axis('off')
plot(mode[1], cmap = cm.ocean)
plt.title('mode {} $h^*$={:.3f}\n $\\lambda_{}$={:.3e} \n $\\Delta E$={:.3e}'
.format(i, h_opts[i], i, stability.eigs[i], en_vars[i]), fontsize= 15)
# plt.title('mode {}'
# .format(i), fontsize= 15)
plt.subplot(2, _nmodes+1, _nmodes+2+1+i)
plt.axis('off')
_pert_beta = mode[1]
_pert_v = mode[0]
if hbounds[i][0] == hbounds[i][1] == 0:
plt.plot(hbounds[i][0], 0)
else:
hs = np.linspace(hbounds[i][0], hbounds[i][1], 100)
z = np.polyfit(np.linspace(hbounds[i][0], hbounds[i][1],
len(en_perts[i])), en_perts[i], parameters['stability']['order'])
p = np.poly1d(z)
plt.plot(hs, p(hs), c='k')
plt.plot(np.linspace(hbounds[i][0], hbounds[i][1],
len(en_perts[i])), en_perts[i], marker='o', markersize=10, c='k')
plt.plot(hs, stability.eigs[i]*hs**2, c='r', lw=.3)
plt.axvline(h_opts[i], lw = .3, c='k')
plt.axvline(0, lw=2, c='k')
# plt.title('{}'.format(i))
plt.tight_layout(h_pad=1.5, pad=1.5)
# plt.legend()
plt.savefig(os.path.join(outdir, "modes-{:.3f}-{}.pdf".format(load, iteration)))
plt.close(fig)
plt.clf()
log(LogLevel.INFO, 'plotted modes')
plt.figure()
plt.plot(mineigs, marker = 'o')
plt.axhline(0.)
plt.savefig(os.path.join(outdir, "mineigs-{:.3f}.pdf".format(load)))
def test_reduced_mesh_save_elliptic_vector(mesh, save_tempdir):
log(PROGRESS, "*** Elliptic case, vector, offline computation ***")
V = EllipticFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, ))
dofs = [(1, ), (11, ), (48, ), (41, )]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_elliptic_vector")
_test_reduced_mesh_elliptic_vector(V, reduced_mesh)
def outputData():
np.save(os.path.join(outdir, 'bifurcation_loads'), bifurcation_loads, allow_pickle=True, fix_imports=True)
with files['output'] as file:
file.write(alpha, load)
file.write(u, load)
with files['postproc'] as file:
file.write_checkpoint(alpha, "alpha-{}".format(step), step, append = True)
file.write_checkpoint(u, "u-{}".format(step), step, append = True)
log(LogLevel.INFO, 'Written postprocessing step {}'.format(step))
time_data_pd.to_json(os.path.join(outdir, "time_data.json"))
def test_reduced_mesh_save_elliptic_matrix(mesh, save_tempdir):
log(PROGRESS, "*** Elliptic case, matrix, offline computation ***")
V = EllipticFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, V))
dofs = [(1, 2), (11, 12), (48, 12), (41, 41)]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_elliptic_matrix")
_test_reduced_mesh_elliptic_matrix(V, reduced_mesh)
def test_reduced_mesh_save_collapsed_vector(mesh, save_tempdir):
log(PROGRESS, "*** Collapsed case, vector, offline computation ***")
(V, _) = CollapsedFunctionSpaces(mesh)
reduced_mesh = ReducedMesh((V, ))
dofs = [(2, ), (48, ), (40, ), (11, )]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_collapsed_vector")
_test_reduced_mesh_collapsed_vector(V, reduced_mesh)
def test_reduced_mesh_save_collapsed_matrix(mesh, save_tempdir):
log(PROGRESS, "*** Collapsed case, matrix, offline computation ***")
(V, U) = CollapsedFunctionSpaces(mesh)
reduced_mesh = ReducedMesh((V, U))
dofs = [(2, 1), (48, 33), (40, 12), (31, 39)]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_collapsed_matrix")
_test_reduced_mesh_collapsed_matrix(V, U, reduced_mesh)
def test_reduced_mesh_save_mixed_vector(mesh, save_tempdir):
log(PROGRESS, "*** Mixed case, vector, offline computation ***")
V = MixedFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, ))
dofs = [(2, ), (33, ), (48, ), (42, )]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_mixed_vector")
_test_reduced_mesh_mixed_vector(V, reduced_mesh)
def test_reduced_mesh_save_mixed_matrix(mesh, save_tempdir):
log(PROGRESS, "*** Mixed case, matrix, offline computation ***")
V = MixedFunctionSpace(mesh)
reduced_mesh = ReducedMesh((V, V))
dofs = [(1, 2), (31, 33), (48, 12), (42, 42)]
for pair in dofs:
log(PROGRESS, "Adding " + str(pair))
reduced_mesh.append(pair)
reduced_mesh.save(save_tempdir, "test_reduced_mesh_mixed_matrix")
_test_reduced_mesh_mixed_matrix(V, reduced_mesh)
def solve(self, alpha_old):
"""
Solves second order problem returning stability flag and number of negative
eigenvalues.
"""
self.alpha_old = alpha_old
self.assigner.assign(self.z, [self.u, self.alpha])
if self.is_elastic():
log(LogLevel.INFO, 'Current state: elastic')
else:
log(LogLevel.INFO, 'Current state: inelastic')
inactive_dofs = self.getInactiveSet()
index_set = self.getFreeDofsIS(inactive_dofs)
print(f'inactive_dofs {inactive_dofs}')
print(f'free_dofs {index_set}')
self.inertia_setup()
negev = self.get_inertia(self._Hessian, restricted_dofs_is=index_set)
eigen = EigenSolver(self.H,
self.z,
restricted_dofs_is=index_set,
slepc_options=self.parameters['eigen'],
initial_guess=self.getInitialGuess())
nconv, it = eigen.solve(
min(self.parameters['stability']['maxmodes'], negev + 1))
eigs = eigen.get_eigenvalues(nconv)
self.sanityCheck(negev, eigs)
_stabilityData = self.postprocEigs(eigs, eigen)
self.compileData(_stabilityData, eigs)
self.i += 1
self.stable = eigs[0, 0].real > float(
self.parameters['eigen']['eig_rtol']) # based on eigenvalue
if self.is_elastic():
self.stable = True
return (self.stable, int(negev))
def __init__(self, problem, parameters={}, lb=None):
super(DamageSolverSNES, self).__init__()
self.problem = problem
self.energy = problem.energy
self.state = problem.state
self.alpha = problem.state['alpha']
self.alpha_dvec = as_backend_type(self.alpha.vector())
self.alpha_pvec = self.alpha_dvec.vec()
self.bcs = problem.bcs
self.parameters = parameters
comm = self.alpha.function_space().mesh().mpi_comm()
self.comm = comm
V = self.alpha.function_space()
self.V = V
self.Ealpha = derivative(
self.energy, self.alpha,
dolfin.TestFunction(self.alpha.ufl_function_space()))
self.dm = self.alpha.function_space().dofmap()
solver = PETScSNESSolver()
snes = solver.snes()
if lb == None:
lb = interpolate(Constant(0.), V)
ub = interpolate(Constant(1.), V)
prefix = "damage_"
snes.setOptionsPrefix(prefix)
for option, value in self.parameters["snes"].items():
PETScOptions.set(prefix + option, value)
log(LogLevel.DEBUG,
"DEBUG: Set: {} = {}".format(prefix + option, value))
snes.setFromOptions()
(J, F, bcs_alpha) = (problem.J, problem.F, problem.bcs)
self.ass = SystemAssembler(J, F, bcs_alpha)
self.b = self.init_residual()
snes.setFunction(self.residual, self.b.vec())
self.A = self.init_jacobian()
snes.setJacobian(self.jacobian, self.A.mat())
snes.ksp.setOperators(self.A.mat())
snes.setVariableBounds(self.problem.lb.vec(), self.problem.ub.vec()) #
# snes.solve(None, Function(V).vector().vec())
self.solver = snes
def test_shared_entities_detection(mesh, submesh, tempdir):
dim_to_text = {
submesh.topology().dim(): "cells",
submesh.topology().dim() - 1: "facets",
0: "vertices"
}
for dim in [submesh.topology().dim(), submesh.topology().dim() - 1, 0]:
shared_entities = submesh.topology().shared_entities(dim)
log(PROGRESS, "Submesh shared indices for " + str(dim_to_text[dim]))
log(PROGRESS, str(shared_entities))
filename = "test_shared_entities_detection__dim_" + str(
dim) + "__size_" + str(MPI.size(
submesh.mpi_comm())) + "_rank_" + str(
MPI.rank(submesh.mpi_comm())) + ".pkl"
dict_save(shared_entities, tempdir, filename)
dict_assert_equal(shared_entities, data_dir, filename)
def test_mesh_to_submesh_global_vertex_indices(mesh, submesh, tempdir):
log(PROGRESS, "Mesh to submesh global vertex indices:")
for (mesh_local_index, submesh_local_index
) in submesh.mesh_to_submesh_vertex_local_indices.items():
mesh_global_index = mesh.topology().global_indices(0)[mesh_local_index]
submesh_global_index = submesh.topology().global_indices(
0)[submesh_local_index]
log(PROGRESS,
"\t" + str(mesh_global_index) + " -> " + str(submesh_global_index))
assert_mesh_plotter(mesh, submesh, "V", tempdir,
"test_mesh_to_submesh_global_vertex_indices")
filename = "test_mesh_to_submesh_global_vertex_indices" + "_size_" + str(
MPI.size(submesh.mpi_comm())) + "_rank_" + str(
MPI.rank(submesh.mpi_comm())) + ".pkl"
dict_save(submesh.mesh_to_submesh_vertex_local_indices, tempdir, filename)
dict_assert_equal(submesh.mesh_to_submesh_vertex_local_indices, data_dir,
filename)
def test_submesh_to_mesh_global_vertex_indices(mesh, submesh, tempdir):
log(PROGRESS, "Submesh to mesh global vertex indices:")
for (submesh_local_index, mesh_local_index) in enumerate(
submesh.submesh_to_mesh_vertex_local_indices):
submesh_global_index = submesh.topology().global_indices(
0)[submesh_local_index]
mesh_global_index = mesh.topology().global_indices(0)[mesh_local_index]
log(PROGRESS,
"\t" + str(submesh_global_index) + " -> " + str(mesh_global_index))
assert_mesh_plotter(mesh, submesh, "V", tempdir,
"test_submesh_to_mesh_global_vertex_indices")
filename = "test_submesh_to_mesh_global_vertex_indices" + "_size_" + str(
MPI.size(submesh.mpi_comm())) + "_rank_" + str(
MPI.rank(submesh.mpi_comm())) + ".pkl"
array_save(submesh.submesh_to_mesh_vertex_local_indices, tempdir, filename)
array_assert_equal(submesh.submesh_to_mesh_vertex_local_indices, data_dir,
filename)
def solve(self):
"""
Solve the damage problem for the current state.
"""
log(LogLevel.INFO, "Solving damage")
try:
self.solver.solve()
return (self.solver.solver.getIterationNumber(),
self.solver.solver.getConvergedReason())
except:
log(LogLevel.WARNING,
"WARNING: Damage solver failed, what's next?")
raise RuntimeError("Damage solvers did not converge")
def __init__(self, energy, state, bcs, parameters={}):
super(ElasticitySolver, self).__init__()
solver_name = 'elasticity'
self.problem = ElasticityProblem(energy, state, bcs)
# Set the solver
self.solver = PETScSNESSolver()
snes = self.solver.snes()
prefix = "elasticity_"
snes.setOptionsPrefix(prefix)
print(parameters)
for parameter, value in parameters.items():
log(LogLevel.DEBUG,
"DEBUG: Set: {} = {}".format(prefix + parameter, value))
PETScOptions.set(prefix + parameter, value)
snes.setFromOptions()
def test_separated_parametrized_forms_vector_14():
a14 = expr14[0]*inner(u, v)*dx
a14_sep = SeparatedParametrizedForm(a14)
log(PROGRESS, "*** ### FORM 14 ### ***")
log(PROGRESS, "This form is similar to form 12, but each term is multiplied by a component of a Function which is not solution of a parametrized problem. This results in no parametrized coefficients")
a14_sep.separate()
log(PROGRESS, "\tLen coefficients:\n" +
"\t\t" + str(len(a14_sep.coefficients)) + "\n"
)
assert 0 == len(a14_sep.coefficients)
log(PROGRESS, "\tLen unchanged forms:\n" +
"\t\t" + str(len(a14_sep._form_unchanged)) + "\n"
)
assert 1 == len(a14_sep._form_unchanged)
log(PROGRESS, "\tUnchanged forms:\n" +
"\t\t" + str(a14_sep._form_unchanged[0].integrals()[0].integrand()) + "\n"
)
assert "f_30[0] * (sum_{i_{154}} v_0[i_{154}] * v_1[i_{154}] )" == str(a14_sep._form_unchanged[0].integrals()[0].integrand())
def get_auxiliary_reduced_function_space(self, auxiliary_problem, component, index=None):
assert isinstance(component, tuple)
assert len(component) > 0
index = self._get_dict_index(index)
auxiliary_V = _sub_from_tuple(auxiliary_problem.V, component)
key = (auxiliary_problem, component, index)
if key not in self._auxiliary_reduced_function_space:
auxiliary_reduced_V = wrapping.convert_functionspace_to_submesh(auxiliary_V, self.reduced_mesh[index], self._get_auxiliary_reduced_function_space_type(auxiliary_V))
self._auxiliary_reduced_function_space[key] = auxiliary_reduced_V
if not self._load_auxiliary_reduced_function_space(key):
# Get the map between DOFs on auxiliary_V and auxiliary_reduced_V
(auxiliary_dofs_to_reduced_dofs, _) = wrapping.map_functionspaces_between_mesh_and_submesh(auxiliary_V, self.mesh, auxiliary_reduced_V, self.reduced_mesh[index])
log(DEBUG, "Auxiliary DOFs to reduced DOFs is " + str(auxiliary_dofs_to_reduced_dofs))
self._auxiliary_dofs_to_reduced_dofs[key] = auxiliary_dofs_to_reduced_dofs
# Save to file
self._save_auxiliary_reduced_function_space(key)
else:
assert key in self._auxiliary_dofs_to_reduced_dofs
return self._auxiliary_reduced_function_space[key]
def jit_generate(cpp_code, module_name, signature, parameters):
log(LogLevel.TRACE, "Calling dijitso just-in-time (JIT) compiler for pybind11 code.")
# Split code on reserved word "SIGNATURE" which will be replaced
# by the module signature
# This must occur only once in the code
split_cpp_code = re.split('SIGNATURE', cpp_code)
if len(split_cpp_code) < 2:
raise RuntimeError("Cannot find keyword: SIGNATURE in pybind11 C++ code.")
elif len(split_cpp_code) > 2:
raise RuntimeError("Found multiple instances of keyword: SIGNATURE in pybind11 C++ code.")
code_c = split_cpp_code[0] + signature + split_cpp_code[1]
code_h = ""
depends = []
return code_h, code_c, depends
def jit_generate(class_data, module_name, signature, parameters):
"""TODO: document"""
template_code = """
// Based on https://gcc.gnu.org/wiki/Visibility
#if defined _WIN32 || defined __CYGWIN__
#ifdef __GNUC__
#define DLL_EXPORT __attribute__ ((dllexport))
#else
#define DLL_EXPORT __declspec(dllexport)
#endif
#else
#define DLL_EXPORT __attribute__ ((visibility ("default")))
#endif
#include <dolfin/function/Expression.h>
#include <dolfin/math/basic.h>
#include <Eigen/Dense>
{math_header}
namespace dolfin
{{
class {classname} : public Expression
{{
public:
{members}
{classname}()
{{
{constructor}
}}
void eval(Eigen::Ref<Eigen::VectorXd> values, Eigen::Ref<const Eigen::VectorXd> x) const override
{{
{statement}
}}
void set_property(std::string name, double _value) override
{{
{set_props}
throw std::runtime_error("No such property");
}}
double get_property(std::string name) const override
{{
{get_props}
throw std::runtime_error("No such property");
return 0.0;
}}
void set_generic_function(std::string name, std::shared_ptr<dolfin::GenericFunction> _value) override
{{
{set_generic_function}
throw std::runtime_error("No such property");
}}
std::shared_ptr<dolfin::GenericFunction> get_generic_function(std::string name) const override
{{
{get_generic_function}
throw std::runtime_error("No such property");
}}
}};
}}
extern "C" DLL_EXPORT dolfin::Expression * create_{classname}()
{{
return new dolfin::{classname};
}}
"""
_get_props = """ if (name == "{key_name}") return {name};"""
_set_props = """ if (name == "{key_name}") {{ {name} = _value; return; }}"""
log(LogLevel.TRACE, "Calling dijitso just-in-time (JIT) compiler for Expression.")
statements = class_data["statements"]
statement = ""
if isinstance(statements, str):
statement += " values[0] = " + statements + ";\n"
else:
for i, val in enumerate(statements):
statement += " values[" + str(i) + "] = " + val + ";\n"
constructor = ""
members = ""
set_props = ""
get_props = ""
set_generic_function = ""
get_generic_function = ""
# Add code for setting and getting property values
properties = class_data["properties"]
for k in properties:
value = properties[k]
if isinstance(value, (float, int)):
members += "double " + k + ";\n"
set_props += _set_props.format(key_name=k, name=k)
get_props += _get_props.format(key_name=k, name=k)
elif hasattr(value, "_cpp_object"):
members += "std::shared_ptr<dolfin::GenericFunction> generic_function_{key};\n".format(key=k)
set_generic_function += _set_props.format(key_name=k,
name="generic_function_" + k)
get_generic_function += _get_props.format(key_name=k,
name="generic_function_" + k)
value_size = value._cpp_object.value_size()
if value_size == 1:
_setup_statement = """ double {key};
generic_function_{key}->eval(Eigen::Map<Eigen::Matrix<double, 1, 1>>(&{key}), x);\n""".format(key=k)
else:
_setup_statement = """ double {key}[{value_size}];
generic_function_{key}->eval(Eigen::Map<Eigen::Matrix<double, {value_size}, 1>>({key}), x);\n""".format(key=k, value_size=value_size)
statement = _setup_statement + statement
# Set the value_shape
for dim in class_data['value_shape']:
constructor += "_value_shape.push_back(" + str(dim) + ");"
classname = signature
code_c = template_code.format(statement=statement,
classname=classname,
members=members,
constructor=constructor,
set_props=set_props,
get_props=get_props,
get_generic_function=get_generic_function,
set_generic_function=set_generic_function,
math_header=_math_header)
code_h = ""
depends = []
return code_h, code_c, depends
def jit_generate(class_data, module_name, signature, parameters):
template_code = """
// Based on https://gcc.gnu.org/wiki/Visibility
#if defined _WIN32 || defined __CYGWIN__
#ifdef __GNUC__
#define DLL_EXPORT __attribute__ ((dllexport))
#else
#define DLL_EXPORT __declspec(dllexport)
#endif
#else
#define DLL_EXPORT __attribute__ ((visibility ("default")))
#endif
#include <dolfin/common/Array.h>
#include <dolfin/math/basic.h>
#include <dolfin/mesh/SubDomain.h>
#include <Eigen/Dense>
{math_header}
namespace dolfin
{{
class {classname} : public SubDomain
{{
public:
{members}
{classname}()
{{
{constructor}
}}
// Return true for points inside the sub domain
bool inside(const Eigen::Ref<const Eigen::VectorXd> x, bool on_boundary) const final
{{
return {inside};
}}
void set_property(std::string name, double value)
{{
{set_props}
}}
double get_property(std::string name) const
{{
{get_props}
return 0.0;
}}
}};
}}
extern "C" DLL_EXPORT dolfin::SubDomain * create_{classname}()
{{
return new dolfin::{classname};
}}
"""
_set_prop = """ if (name == "{name}") {name} = value;\n"""
_get_prop = """ if (name == "{name}") return {name};\n"""
log(LogLevel.TRACE, "Calling dijitso just-in-time (JIT) compiler for SubDomain.")
inside_code = class_data['statements'][0]
members = ""
get_props = ""
set_props = ""
for k in class_data['properties']:
members += " double " + k + ";\n"
get_props += _get_prop.format(name=k)
set_props += _set_prop.format(name=k)
classname = signature
code_c = template_code.format(inside=inside_code,
classname=classname,
math_header=_math_header,
members=members, constructor="",
get_props=get_props,
set_props=set_props)
code_h = ""
depends = []
return code_h, code_c, depends