Hello,
I am running a code to study phase transformations in metals. The code runs
without any problem in release mode, but gives nan when outputting stress
values using the same code snippet as in Step-18.
When I run the same code in debug mode, it gives the following error:
An error occurred in line <2183> of file
</home/rnp/Software/dealii-build/deal.II-v9.3.3/include/deal.II/lac/affine_constraints.h>
in function
dealii::types::global_dof_index
dealii::AffineConstraints<number>::calculate_line_index(dealii::AffineConstraints<number>::size_type)
const [with number = double; dealii::types::global_dof_index = unsigned
int; dealii::AffineConstraints<number>::size_type = unsigned int]
The violated condition was:
local_lines.is_element(line_n)
Additional information:
The index set given to this constraints object indicates constraints
for degree of freedom 31328 should not be stored by this object, but a
constraint is being added.
Stacktrace:
-----------
#0 microPF_polycrystal:
dealii::AffineConstraints<double>::calculate_line_index(unsigned int) const
#1 microPF_polycrystal:
dealii::AffineConstraints<double>::is_constrained(unsigned int) const
#2
/home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3:
dealii::AffineConstraints<double>::make_sorted_row_list(std::vector<unsigned
int, std::allocator<unsigned int> > const&, std::vector<unsigned int,
std::allocator<unsigned int> >&) const
#3
/home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3:
void
dealii::AffineConstraints<double>::add_entries_local_to_global<dealii::DynamicSparsityPattern>(std::vector<unsigned
int, std::allocator<unsigned int> > const&,
dealii::DynamicSparsityPattern&, bool, dealii::Table<2, bool> const&,
std::integral_constant<bool, false>) const
#4
/home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3:
void
dealii::AffineConstraints<double>::add_entries_local_to_global<dealii::DynamicSparsityPattern>(std::vector<unsigned
int, std::allocator<unsigned int> > const&,
dealii::DynamicSparsityPattern&, bool, dealii::Table<2, bool> const&) const
#5
/home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3:
void dealii::DoFTools::make_sparsity_pattern<3, 3,
dealii::DynamicSparsityPattern, double>(dealii::DoFHandler<3, 3> const&,
dealii::DynamicSparsityPattern&, dealii::AffineConstraints<double> const&,
bool, unsigned int)
#6 microPF_polycrystal: PhaseField::Solid<3>::setup_system()
#7 microPF_polycrystal: PhaseField::Solid<3>::run()
#8 microPF_polycrystal: main
--------------------------------------------------------
It points to a problem in defining constraints in setup_system. But I
believe I defined the constraints correctly. I have a similar code that
works perfectly and the only thing I have changed is adding grain
orientations which do not effect the constraint definition.
Is my understanding of the error message correct? Is there something that I
am missing in debugging the code?
Below is the code snippet of setup_system -
template <int dim>
void Solid<dim>::setup_system()
{
TimerOutput::Scope t(computing_timer, "setup");
dof_handler.distribute_dofs(fe);
dof_handler_c.distribute_dofs(fe_c);
history_dof_handler.distribute_dofs(history_fe);
// DoFRenumbering::Cuthill_McKee(dof_handler);
const unsigned int n_dofs = dof_handler.n_dofs();
const unsigned int n_dofs_c = dof_handler_c.n_dofs();
// Number of active cells and DoFs
pcout << " Number of active cells: "
<< triangulation.n_active_cells()
<< std::endl
<< " Number of degrees of freedom: "
<< n_dofs + n_dofs_c
<< " (" << n_dofs << '+' << n_dofs_c << ')'
<< std::endl;
locally_owned_dofs = dof_handler.locally_owned_dofs();
DoFTools::extract_locally_relevant_dofs(dof_handler,
locally_relevant_dofs);
constraints.clear();
constraints.reinit(locally_relevant_dofs);
{
DoFTools::make_periodicity_constraints(dof_handler, 0, 1, 0,
constraints);
DoFTools::make_periodicity_constraints(dof_handler, 2, 3, 1,
constraints);
DoFTools::make_periodicity_constraints(dof_handler, 4, 5, 2,
constraints);
}
constraints.close();
// constraints.print(std::cout);
DynamicSparsityPattern dsp(locally_relevant_dofs);
DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints,
false);
Utilities::MPI::all_gather(mpi_communicator,
dof_handler.locally_owned_dofs());
SparsityTools::distribute_sparsity_pattern (dsp,
dof_handler.locally_owned_dofs(),
mpi_communicator,
locally_relevant_dofs);
tangent_matrix.reinit(locally_owned_dofs, locally_owned_dofs, dsp,
mpi_communicator);
solution.reinit(locally_owned_dofs, locally_relevant_dofs,
mpi_communicator);
solution_update.reinit(locally_owned_dofs, locally_relevant_dofs,
mpi_communicator);
system_rhs.reinit(locally_owned_dofs, mpi_communicator);
locally_owned_dofs_c = dof_handler_c.locally_owned_dofs();
DoFTools::extract_locally_relevant_dofs(dof_handler_c,
locally_relevant_dofs_c);
constraints_c.clear();
constraints_c.reinit(locally_relevant_dofs);
{
// DoFTools::make_periodicity_constraints(dof_handler_c, 0, 1,
0, constraints_c);
// DoFTools::make_periodicity_constraints(dof_handler_c, 2, 3,
1, constraints_c);
// DoFTools::make_periodicity_constraints(dof_handler_c, 4, 5,
2, constraints_c);
}
constraints_c.close();
DynamicSparsityPattern dsp_c(locally_relevant_dofs_c);
DoFTools::make_sparsity_pattern(dof_handler_c, dsp_c,
constraints_c, true);
Utilities::MPI::all_gather(mpi_communicator,
dof_handler_c.locally_owned_dofs());
SparsityTools::distribute_sparsity_pattern (dsp_c,
dof_handler_c.locally_owned_dofs(),
mpi_communicator,
locally_relevant_dofs_c);
mass_matrix.reinit(locally_owned_dofs_c, locally_owned_dofs_c,
dsp_c, mpi_communicator);
solution_c0.reinit(locally_owned_dofs_c, locally_relevant_dofs_c,
mpi_communicator);
solution_c1.reinit(locally_owned_dofs_c, locally_relevant_dofs_c,
mpi_communicator);
solution_c2.reinit(locally_owned_dofs_c, locally_relevant_dofs_c,
mpi_communicator);
solution_c3.reinit(locally_owned_dofs_c, locally_relevant_dofs_c,
mpi_communicator);
system_rhs_c1.reinit(locally_owned_dofs_c, mpi_communicator);
system_rhs_c2.reinit(locally_owned_dofs_c, mpi_communicator);
system_rhs_c3.reinit(locally_owned_dofs_c, mpi_communicator); }
Thanks in advance,
Raghunandan.
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