void make_grid_and_dofs ();
void oldstyle_operation ();
void assemble_system ();
- void output_results (const unsigned int timestep_number) const;
+ void output_results (const unsigned int timestep_number);
#ifdef DEAL_II_WITH_P4EST
parallel::distributed::Triangulation<dim> triangulation;
// This function prints the norm of the solution and writes the solution
// vector to a file. The norm is standard (except for the fact that we need
// to be sure to only count norms on locally owned cells), and the second is
- // similar to what we did in step-40. However, we first need to generate an
- // appropriate vector for output: The ones we used during time stepping
- // contained information about ghosts dofs that one needs write access to
- // during the loops over cell. However, that is not the same as needed when
- // outputting. So we first initialize a vector with locally relevant degrees
- // of freedom by copying the solution (note how we use the function @p
- // copy_from to transfer data between vectors with the same local range, but
- // different layouts of ghosts). Then, we import the values on the ghost
- // DoFs and then distribute the constraints (as constraints are zero in the
- // vectors during loop over all cells).
+ // similar to what we did in step-40. Note that we can use the same vector
+ // for output as we used for computation: The vectors in the matrix-free
+ // framework always provide full information on all locally owned cells
+ // (this is what is needed in the local evaluations, too), including ghost
+ // vector entries on these cells. This is the only data that is needed in
+ // the integrate_difference function as well as in DataOut. We only need to
+ // make sure that we tell the vector to update its ghost values before we
+ // read them. This is a feature present only in the
+ // parallel::distributed::Vector class. Distributed vectors with PETSc and
+ // Trilinos, on the other hand, need to be copied to special vectors
+ // including ghost values (see the relevant section in step-40). If we
+ // wanted to access all degrees of freedom on ghost cells, too (e.g. when
+ // computing error estimators that use the jump of solution over cell
+ // boundaries), we would need more information and create a vector
+ // initialized with locally relevant dofs just as in step-40. Observe also
+ // that we need to distribute constraints for output - they are not filled
+ // during computations (rather, they are distributed on the fly in the
+ // matrix-free method read_dof_values).
template <int dim>
void
- SineGordonProblem<dim>::output_results (const unsigned int timestep_number) const
+ SineGordonProblem<dim>::output_results (const unsigned int timestep_number)
{
- parallel::distributed::Vector<double> locally_relevant_solution;
- locally_relevant_solution.reinit (dof_handler.locally_owned_dofs(),
- locally_relevant_dofs,
- MPI_COMM_WORLD);
- locally_relevant_solution.copy_from (solution);
- locally_relevant_solution.update_ghost_values();
- constraints.distribute (locally_relevant_solution);
+ constraints.distribute (solution);
Vector<float> norm_per_cell (triangulation.n_active_cells());
- locally_relevant_solution.update_ghost_values();
+ solution.update_ghost_values();
VectorTools::integrate_difference (dof_handler,
- locally_relevant_solution,
+ solution,
ZeroFunction<dim>(),
norm_per_cell,
QGauss<dim>(fe_degree+1),
DataOut<dim> data_out;
data_out.attach_dof_handler (dof_handler);
- data_out.add_data_vector (locally_relevant_solution, "solution");
+ data_out.add_data_vector (solution, "solution");
data_out.build_patches ();
const std::string filename =
// the finest mesh size. The finest mesh size is computed as the diameter of
// the last cell in the triangulation, which is the last cell on the finest
// level of the mesh. This is only possible for Cartesian meshes, otherwise,
- // one needs to loop over all cells). Note that we need to query all the
+ // one needs to loop over all cells. Note that we need to query all the
// processors for their finest cell since the not all processors might hold
// a region where the mesh is at the finest level. Then, we readjust the
- // time step a little to hit the final time exactly if necessary.
+ // time step a little to hit the final time exactly.
template <int dim>
void
SineGordonProblem<dim>::run ()
//
// Note how this shift is implemented: We simply call the swap method on
// the two vectors which swaps only some pointers without the need to copy
- // data around. Obviously, this is a more efficient way to move data
- // around. Let us see what happens in more detail: First, we exchange
- // <code>old_solution</code> with <code>old_old_solution</code>, which
- // means that <code>old_old_solution</code> gets
- // <code>old_solution</code>, which is what we expect. Similarly,
- // <code>old_solution</code> gets the content from <code>solution</code>
- // in the next step. Afterward, <code>solution</code> holds
- // <code>old_old_solution</code>, but that will be overwritten during this
- // step.
+ // data around. Obviously, this is a more efficient way to update the
+ // vectors during time stepping. Let us see what happens in more detail:
+ // First, we exchange <code>old_solution</code> with
+ // <code>old_old_solution</code>, which means that
+ // <code>old_old_solution</code> gets <code>old_solution</code>, which is
+ // what we expect. Similarly, <code>old_solution</code> gets the content
+ // from <code>solution</code> in the next step. Afterward,
+ // <code>solution</code> holds <code>old_old_solution</code>, but that
+ // will be overwritten during this step.
unsigned int timestep_number = 1;
Timer timer;
{
namespace
{
- // TODO: in general we should iterate over the constraints and not over all DoFs
- // for performance reasons
template<class VEC>
- void set_zero_parallel(const dealii::ConstraintMatrix &cm, VEC &vec, unsigned int shift = 0)
+ void set_zero_parallel(const std::vector<unsigned int> &cm, VEC &vec, unsigned int shift = 0)
{
Assert(!vec.has_ghost_elements(), ExcInternalError());//ExcGhostsPresent());
-
- const unsigned int
- start = vec.local_range().first,
- end = vec.local_range().second;
- for (unsigned int i=start; i<end; ++i)
- if (cm.is_constrained (shift + i))
- vec(i) = 0;
+ IndexSet locally_owned = vec.locally_owned_elements();
+ for (typename std::vector<unsigned int>::const_iterator it = cm.begin();
+ it != cm.end(); ++it)
+ if (locally_owned.is_element(*it))
+ vec(*it) = 0.;
}
- // TODO: in general we should iterate over the constraints and not over all DoFs
- // for performance reasons
template<typename Number>
- void set_zero_parallel(const dealii::ConstraintMatrix &cm, parallel::distributed::Vector<Number> &vec, unsigned int shift = 0)
+ void set_zero_parallel(const std::vector<unsigned int> &cm, parallel::distributed::Vector<Number> &vec, unsigned int shift = 0)
{
- for (unsigned int i=0; i<vec.local_size(); ++i)
- if (cm.is_constrained (shift + vec.local_range().first+i))
- vec.local_element(i) = 0;
+ for (typename std::vector<unsigned int>::const_iterator it = cm.begin();
+ it != cm.end(); ++it)
+ if (vec.in_local_range(*it))
+ vec(*it) = 0.;
vec.zero_out_ghosts();
}
template<class VEC>
- void set_zero_in_parallel(const dealii::ConstraintMatrix &cm, VEC &vec, internal::bool2type<false>)
+ void set_zero_in_parallel(const std::vector<unsigned int> &cm, VEC &vec, internal::bool2type<false>)
{
set_zero_parallel(cm, vec, 0);
}
// in parallel for BlockVectors
template<class VEC>
- void set_zero_in_parallel(const dealii::ConstraintMatrix &cm, VEC &vec, internal::bool2type<true>)
+ void set_zero_in_parallel(const std::vector<unsigned int> &cm, VEC &vec, internal::bool2type<true>)
{
unsigned int start_shift = 0;
for (unsigned int j=0; j<vec.n_blocks(); ++j)
}
template<class VEC>
- void set_zero_serial(const dealii::ConstraintMatrix &cm, VEC &vec)
+ void set_zero_serial(const std::vector<unsigned int> &cm, VEC &vec)
{
- // TODO would be faster:
- /* std::vector<dealii::ConstraintMatrix::ConstraintLine>::const_iterator constraint_line = cm.lines.begin();
- for (; constraint_line!=cm.lines.end(); ++constraint_line)
- vec(constraint_line->line) = 0.;*/
- for (unsigned int i=0; i<vec.size(); ++i)
- if (cm.is_constrained (i))
- vec(i) = 0;
+ for (typename std::vector<unsigned int>::const_iterator it = cm.begin();
+ it != cm.end(); ++it)
+ vec(*it) = 0.;
}
template<class VEC>
- void set_zero_all(const dealii::ConstraintMatrix &cm, VEC &vec)
+ void set_zero_all(const std::vector<unsigned int> &cm, VEC &vec)
{
set_zero_in_parallel<VEC>(cm, vec, internal::bool2type<IsBlockVector<VEC>::value>());
vec.compress(VectorOperation::insert);
template<class T>
- void set_zero_all(const dealii::ConstraintMatrix &cm, dealii::Vector<T> &vec)
+ void set_zero_all(const std::vector<unsigned int> &cm, dealii::Vector<T> &vec)
{
set_zero_serial(cm, vec);
}
template<class T>
- void set_zero_all(const dealii::ConstraintMatrix &cm, dealii::BlockVector<T> &vec)
+ void set_zero_all(const std::vector<unsigned int> &cm, dealii::BlockVector<T> &vec)
{
set_zero_serial(cm, vec);
}
void
ConstraintMatrix::set_zero (VectorType &vec) const
{
- internal::ConstraintMatrix::set_zero_all(*this, vec);
+ // since we lines is a private member, we cannot pass it to the functions
+ // above. therefore, copy the content which is cheap
+ std::vector<unsigned int> constrained_lines(lines.size());
+ for (unsigned int i=0; i<lines.size(); ++i)
+ constrained_lines[i] = lines[i].line;
+ internal::ConstraintMatrix::set_zero_all(constrained_lines, vec);
}
for (unsigned int i=row+1; i<n_rows; ++i)
old_line.push_back (i-shift);
break;
- };
+ }
}
else
old_line.push_back (row-shift);
parallel::distributed::Vector<number> &output,
const internal::bool2type<false> /*is_block_vector*/)
{
+ const_cast<parallel::distributed::Vector<number>&>(vec).zero_out_ghosts();
output.reinit (locally_owned_elements, needed_elements, vec.get_mpi_communicator());
output = vec;
+ output.update_ghost_values();
}
else if (vector->Map().NumMyElements() > 0)
{
const unsigned int n_indices = vector->Map().NumMyElements();
- int * vector_indices = vector->Map().MyGlobalElements();
- unsigned int range_start = vector_indices[0];
- unsigned int range_end = range_start+1;
- for (unsigned int i=1; i<n_indices; ++i, ++range_end)
- if (static_cast<unsigned int>(vector_indices[i]) != range_end)
- {
- is.add_range(range_start, range_end);
- range_end = range_start = vector_indices[i];
- }
- is.add_range(range_start, range_end);
+ unsigned int * vector_indices = (unsigned int*)vector->Map().MyGlobalElements();
+ is.add_indices(vector_indices, vector_indices+n_indices);
is.compress();
}
void make_grid_and_dofs ();
void oldstyle_operation ();
void assemble_system ();
- void output_results (const unsigned int timestep_number) const;
+ void output_results (const unsigned int timestep_number);
parallel::distributed::Triangulation<dim> triangulation;
FE_Q<dim> fe;
template <int dim>
void
- SineGordonProblem<dim>::output_results (const unsigned int timestep_number) const
+ SineGordonProblem<dim>::output_results (const unsigned int timestep_number)
{
- parallel::distributed::Vector<double> locally_relevant_solution;
- locally_relevant_solution.reinit (dof_handler.locally_owned_dofs(),
- locally_relevant_dofs,
- MPI_COMM_WORLD);
- locally_relevant_solution.copy_from (solution);
- locally_relevant_solution.update_ghost_values();
- constraints.distribute (locally_relevant_solution);
+ constraints.distribute (solution);
+ solution.update_ghost_values();
Vector<float> norm_per_cell (triangulation.n_active_cells());
- locally_relevant_solution.update_ghost_values();
VectorTools::integrate_difference (dof_handler,
- locally_relevant_solution,
+ solution,
ZeroFunction<dim>(),
norm_per_cell,
QGauss<dim>(fe_degree+1),
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