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Merged
fdrmrc merged 3 commits into from
Apr 26, 2026
Merged

Allow to read fiber data from external file #157

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1085f62
Fix compilation with latest deal.II master.
fdrmrc Mar 23, 2026
4e06a70
Working version with fibers
fdrmrc Mar 28, 2026
dcb1322
Add block-Jacobi as preconditioner. Allow computation of conduction v…
fdrmrc Mar 31, 2026
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11 changes: 6 additions & 5 deletions examples/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,15 @@ FOREACH(_build_type ${_d2_build_types})

# Require MUMPS for monodomain examples
if(exename STREQUAL "monodomain_DG3D" OR exename STREQUAL "monodomain_DG2D")
if(NOT DEAL_II_WITH_MUMPS)
if(NOT DEAL_II_WITH_MUMPS OR NOT DEAL_II_WITH_HDF5)
message(WARNING "\n"
"*** The example '${exename}' requires MUMPS support. ***\n\n"
"Please recompile deal.II with MUMPS enabled for this example to work correctly.\n"
"To enable MUMPS in deal.II, use -DDEAL_II_WITH_MUMPS=ON when configuring deal.II."
"*** The example '${exename}' requires MUMPS and HDF5 support. ***\n\n"
"Please recompile deal.II with MUMPS and HDF5 enabled for this example to work correctly.\n"
"To enable MUMPS in deal.II, use -DDEAL_II_WITH_MUMPS=ON when configuring deal.II.\n"
"To enable HDF5 in deal.II, use -DDEAL_II_WITH_HDF5=ON when configuring deal.II."
)
else()
message("-- MUMPS support detected for ${exename}")
message("-- MUMPS and HDF5 support detected for ${exename}")
endif()
endif()

Expand Down
116 changes: 81 additions & 35 deletions examples/monodomain_DG2D.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ static constexpr unsigned int starting_level = 1;

// matrix-free related parameters
static constexpr bool use_matrix_free_action = true;
static constexpr unsigned int degree_finite_element = 1;
static constexpr unsigned int degree_finite_element = 4;
constexpr unsigned int n_qpoints = degree_finite_element + 1;
static constexpr unsigned int n_components = 1;

Expand Down Expand Up @@ -191,16 +191,40 @@ namespace Utils

} // namespace Utils

enum class PreconditionerType
{
amg,
agglomg,
block_jacobi
};

inline std::string
preconditioner_type_to_string(const PreconditionerType type)
{
switch (type)
{
case PreconditionerType::amg:
return "AMG";
case PreconditionerType::agglomg:
return "AGGLOMG";
case PreconditionerType::block_jacobi:
return "BLOCKJACOBI";
default:
DEAL_II_NOT_IMPLEMENTED();
return "";
}
}

// Model parameters for FitzHugh-Nagumo
struct ModelParameters
{
SolverControl control;
bool use_amg_preconditioner = true;
unsigned int output_frequency = 4001;
bool output_results = true;
double dt = 1e-4;
double final_time = dt * 20;
double final_time_current = 3e-3;
SolverControl control;
PreconditionerType preconditioner_type = PreconditionerType::block_jacobi;
unsigned int output_frequency = 4001;
bool output_results = false;
double dt = 1e-4;
double final_time = 0.4;
double final_time_current = 3e-3;


double penalty_constant = 10.;
Expand Down Expand Up @@ -466,6 +490,7 @@ class IonicModel
SparsityPattern sparsity;
AffineConstraints<double> constraints;
TrilinosWrappers::PreconditionAMG amg_preconditioner;
TrilinosWrappers::PreconditionILU block_jacobi_preconditioner;
TrilinosWrappers::SparseMatrix mass_matrix;
TrilinosWrappers::SparseMatrix laplace_matrix;

Expand Down Expand Up @@ -721,9 +746,8 @@ IonicModel<dim>::setup_problem()
communicator);

file_iterations.open(
"iterations_" +
std::string(param.use_amg_preconditioner ? "AMG" : "AGGLOMG") + "_level_" +
std::to_string(total_tree_levels + 1) + "_" +
"iterations_" + preconditioner_type_to_string(param.preconditioner_type) +
"_level_" + std::to_string(total_tree_levels + 1) + "_" +
std::to_string(Utilities::MPI::n_mpi_processes(communicator)) +
"_procs_deg_" + std::to_string(dg_fe.degree) + ".txt");
}
Expand Down Expand Up @@ -1264,16 +1288,27 @@ IonicModel<dim>::solve()

if constexpr (measure_solve_times)
start_solver = MPI_Wtime();
if (param.use_amg_preconditioner)
solver.solve(system_operator,
locally_relevant_solution_current,
system_rhs,
amg_preconditioner);
else
solver.solve(system_operator,
locally_relevant_solution_current,
system_rhs,
*preconditioner);
switch (param.preconditioner_type)
{
case PreconditionerType::amg:
solver.solve(system_operator,
locally_relevant_solution_current,
system_rhs,
amg_preconditioner);
break;
case PreconditionerType::block_jacobi:
solver.solve(system_operator,
locally_relevant_solution_current,
system_rhs,
block_jacobi_preconditioner);
break;
case PreconditionerType::agglomg:
solver.solve(system_operator,
locally_relevant_solution_current,
system_rhs,
*preconditioner);
break;
}

if constexpr (measure_solve_times)
{
Expand Down Expand Up @@ -1416,23 +1451,34 @@ IonicModel<dim>::run()

pcout << "Max mesh size: " << mesh_size << std::endl;

// Use AMG or agglomeration-based multigrid
if (param.use_amg_preconditioner)
// Use AMG, block-Jacobi, or agglomeration-based multigrid
switch (param.preconditioner_type)
{
typename TrilinosWrappers::PreconditionAMG::AdditionalData amg_data;
if (dg_fe.degree > 1)
amg_data.higher_order_elements = true;

amg_data.aggregation_threshold = 0.1; // 0.15;
amg_data.smoother_type = "Chebyshev";
amg_data.smoother_sweeps = 3;
amg_data.output_details = true;
amg_preconditioner.initialize(*system_matrix, amg_data);
case PreconditionerType::amg:
{
typename TrilinosWrappers::PreconditionAMG::AdditionalData amg_data;
if (dg_fe.degree > 1)
amg_data.higher_order_elements = true;

amg_data.aggregation_threshold = 0.1; // 0.15;
amg_data.smoother_type = "Chebyshev";
amg_data.smoother_sweeps = 3;
amg_data.output_details = true;
amg_preconditioner.initialize(*system_matrix, amg_data);
break;
}
case PreconditionerType::block_jacobi:
{
typename TrilinosWrappers::PreconditionILU::AdditionalData ilu_data;
block_jacobi_preconditioner.initialize(*system_matrix, ilu_data);
break;
}
case PreconditionerType::agglomg:
setup_multigrid();
break;
}
else
setup_multigrid();

pcout << "Setup multigrid preconditioner: done " << std::endl;
pcout << "Setup preconditioner: done " << std::endl;

while (time <= end_time)
{
Expand Down
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