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Remove Kelly-based AMR
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@Rombur
Rombur committed Apr 19, 2024
1 parent 3506b0d commit 6715a97
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Showing 13 changed files with 43 additions and 171 deletions.
9 changes: 2 additions & 7 deletions README.md
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Expand Up @@ -138,14 +138,9 @@ The following options are available:
fields being written to the output files (default value: 1)
* additional\_output\_refinement: additional levels of refinement for the output (default: 0)
* refinement (required):
* n\_heat\_refinements: number of coarsening/refinement to execute (default value: 2)
* heat\_cell\_ratio: this is the ratio (n new cells)/(n old cells) after heat
refinement (default value: 1)
* n\_beam\_refinements: number of times the cells on the paths of the beams
are refined (default value: 2)
* n\_refinements: number of times the cells on the paths of the beams are refined (default value: 2)
* beam\_cutoff: the cutoff value of the heat source terms above which beam-based refinement occurs (default value: 1e-15)
* coarsen\_after\_beam: whether to coarsen cells where the beam has already passed (may conflict with heat refinement, default value: false)
* max\_level: maximum number of times a cell can be refined
* coarsen\_after\_beam: whether to coarsen cells where the beam has already passed (default value: false)
* time\_steps\_between\_refinement: number of time steps after which the
refinement process is performed (default value: 2)
* sources (required):
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104 changes: 11 additions & 93 deletions application/adamantine.hh
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Expand Up @@ -184,51 +184,6 @@ void output_pvtu(
timers[adamantine::output].stop();
}

template <int dim, typename MemorySpaceType,
std::enable_if_t<
std::is_same<MemorySpaceType, dealii::MemorySpace::Host>::value,
int> = 0>
dealii::Vector<float> estimate_error(
dealii::parallel::distributed::Triangulation<dim> const &triangulation,
dealii::DoFHandler<dim> const &dof_handler, int fe_degree,
dealii::LA::distributed::Vector<double, MemorySpaceType> const &solution)
{
dealii::Vector<float> estimated_error_per_cell(
triangulation.n_active_cells());
dealii::KellyErrorEstimator<dim>::estimate(
dof_handler, dealii::QGauss<dim - 1>(fe_degree + 1),
std::map<dealii::types::boundary_id,
const dealii::Function<dim, double> *>(),
solution, estimated_error_per_cell, dealii::ComponentMask(), nullptr, 0,
triangulation.locally_owned_subdomain());

return estimated_error_per_cell;
}

template <int dim, typename MemorySpaceType,
std::enable_if_t<std::is_same<MemorySpaceType,
dealii::MemorySpace::Default>::value,
int> = 0>
dealii::Vector<float> estimate_error(
dealii::parallel::distributed::Triangulation<dim> const &triangulation,
dealii::DoFHandler<dim> const &dof_handler, int fe_degree,
dealii::LA::distributed::Vector<double, MemorySpaceType> const &solution)
{
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
solution_host(solution.get_partitioner());
solution_host.import(solution, dealii::VectorOperation::insert);
dealii::Vector<float> estimated_error_per_cell(
triangulation.n_active_cells());
dealii::KellyErrorEstimator<dim>::estimate(
dof_handler, dealii::QGauss<dim - 1>(fe_degree + 1),
std::map<dealii::types::boundary_id,
const dealii::Function<dim, double> *>(),
solution_host, estimated_error_per_cell, dealii::ComponentMask(), nullptr,
0, triangulation.locally_owned_subdomain());

return estimated_error_per_cell;
}

// inlining this function so we can have in the header
inline void initialize_timers(MPI_Comm const &communicator,
std::vector<adamantine::Timer> &timers)
Expand Down Expand Up @@ -626,56 +581,10 @@ void refine_mesh(
CALI_CXX_MARK_FUNCTION;
#endif
dealii::DoFHandler<dim> &dof_handler = thermal_physics->get_dof_handler();
// Use the Kelly error estimator to refine the mesh. This is done so that the
// part of the domain that were heated stay refined.
// PropertyTreeInput refinement.n_heat_refinements
unsigned int const n_kelly_refinements =
refinement_database.get("n_heat_refinements", 2);
double coarsening_fraction = 0.3;
double refining_fraction = 0.6;
// PropertyTreeInput refinement.heat_cell_ratio
double cells_fraction = refinement_database.get("heat_cell_ratio", 1.);
dealii::parallel::distributed::Triangulation<dim> &triangulation =
dynamic_cast<dealii::parallel::distributed::Triangulation<dim> &>(
const_cast<dealii::Triangulation<dim> &>(
dof_handler.get_triangulation()));
// Number of times the mesh on the beam paths will be refined and maximum
// number of time a cell can be refined.
// PropertyTreeInput refinement.n_beam_refinements
unsigned int const n_beam_refinements =
refinement_database.get("n_beam_refinements", 2);
// PropertyTreeInput refinement.max_level
int max_level = refinement_database.get<int>("max_level");

// PropertyTreeInput refinement.beam_cutoff
const double refinement_beam_cutoff =
refinement_database.get<double>("beam_cutoff", 1.0e-15);

for (unsigned int i = 0; i < n_kelly_refinements; ++i)
{
// Estimate the error. For simplicity, always use dealii::QGauss
dealii::Vector<float> estimated_error_per_cell =
estimate_error(triangulation, dof_handler, fe_degree, solution);

// Flag the cells for refinement.
unsigned int new_n_cells = static_cast<unsigned int>(
cells_fraction *
static_cast<double>(triangulation.n_global_active_cells()));
dealii::GridRefinement::refine_and_coarsen_fixed_fraction(
triangulation, estimated_error_per_cell, refining_fraction,
coarsening_fraction, new_n_cells);

// Don't refine cells that are already as much refined as it is allowed.
for (auto cell :
dealii::filter_iterators(triangulation.active_cell_iterators(),
dealii::IteratorFilters::LocallyOwnedCell()))
if (cell->level() >= max_level)
cell->clear_refine_flag();

// Execute the refinement and transfer the solution onto the new mesh.
refine_and_transfer(thermal_physics, material_properties, dof_handler,
solution);
}

// Refine the mesh along the trajectory of the sources.
double current_source_height =
Expand All @@ -692,7 +601,15 @@ void refine_mesh(
dealii::QGaussLobatto<1>> *>(thermal_physics.get())
->get_current_source_height();

for (unsigned int i = 0; i < n_beam_refinements; ++i)
// PropertyTreeInput refinement.n_refinements
unsigned int const n_refinements =
refinement_database.get("n_refinements", 2);

// PropertyTreeInput refinement.beam_cutoff
const double refinement_beam_cutoff =
refinement_database.get<double>("beam_cutoff", 1.0e-15);

for (unsigned int i = 0; i < n_refinements; ++i)
{
// Compute the cells to be refined.
std::vector<typename dealii::parallel::distributed::Triangulation<
Expand Down Expand Up @@ -722,7 +639,8 @@ void refine_mesh(
{
if (coarsen_after_beam)
cell->clear_coarsen_flag();
if (cell->level() < max_level)

if (cell->level() < static_cast<int>(n_refinements))
cell->set_refine_flag();
}

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7 changes: 2 additions & 5 deletions application/input.info
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Expand Up @@ -22,11 +22,8 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
n_beam_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
max_level 2 ; Maximum number of time a cell can be refined
n_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
}

materials
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10 changes: 3 additions & 7 deletions tests/data/amr_test.info
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Expand Up @@ -23,14 +23,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 1 ; Number of time the cells on the paths of the beams are
; refined
max_level 1 ; Maximum number of time a cell can be refined
n_refinements 1 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 200 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/bare_plate_L_da.info
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Expand Up @@ -52,14 +52,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 1 ; Number of time the cells on the paths of the beams are
; refined
max_level 1 ; Maximum number of time a cell can be refined
n_refinements 1 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 250 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/bare_plate_L_da_augmented.info
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Expand Up @@ -53,14 +53,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 2000000000 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/bare_plate_L_ensemble.info
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Expand Up @@ -30,14 +30,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 2000000000 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/demo_316_short.info
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Expand Up @@ -30,14 +30,10 @@ physics

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 2000000000 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/demo_316_short_anisotropic.info
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Expand Up @@ -30,14 +30,10 @@ physics

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 2000000000 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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7 changes: 2 additions & 5 deletions tests/data/integration_2d.info
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Expand Up @@ -16,11 +16,8 @@ physics

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
n_beam_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
max_level 2 ; Maximum number of time a cell can be refined
n_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
}

materials
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7 changes: 2 additions & 5 deletions tests/data/integration_2d_ensemble.info
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Expand Up @@ -22,11 +22,8 @@ physics

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
n_beam_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
max_level 2 ; Maximum number of time a cell can be refined
n_refinements 2 ; Number of time the cells on the paths of the beams are
; refined
}

materials
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10 changes: 3 additions & 7 deletions tests/data/integration_da_add_material.info
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Expand Up @@ -62,14 +62,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 200000 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
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10 changes: 3 additions & 7 deletions tests/data/thermoelastic_bare_plate.info
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Expand Up @@ -43,14 +43,10 @@ boundary

refinement
{
n_heat_refinements 0 ; Number of coarsening/refinement executed (uses Kelly's
; error estimator)
heat_cell_ratio 2.0 ;
n_beam_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
max_level 0 ; Maximum number of time a cell can be refined
n_refinements 0 ; Number of time the cells on the paths of the beams are
; refined
time_steps_between_refinement 100 ; number of time steps after which
; the refinement process is performed
; the refinement process is performed
}

materials
Expand Down

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