Pratoori:
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:
If your program generates an error in debug mode, nothing you compute in
release mode can be trusted. In other words, it is not worth thinking about
the NaN issue until you have figured this out.
It points to a problem in defining constraints in setup_system.
Actually, it states that the error happens in building the sparsity pattern.
which appears to reference constrained degrees of freedom that aren't stored
in the AffineConstraints object. Why this is so, I can't say -- we'd need to
see the full code, or even better a reduced test case that has everything not
necessary to recreate the code removed.
As for the code snippet, I don't see anything specific that looks wrong
except...
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());
...this line: Utilities::MPI::all_gather() returns the combined results of the
operation as a vector. Calling the function without capturing the return does
nothing useful and only serves to burn CPU time.
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);
And this looks wrong too: You want to initialize constraints_c with
locally_relevant_dofs_c, not locally_relevant_dofs.
Best
W.
--
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Wolfgang Bangerth email: [email protected]
www: http://www.math.colostate.edu/~bangerth/
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