CArl_assemble_coupling.cpp File Reference

Implementation of the parallel coupling matrices assembly. More...

#include "CArl_assemble_coupling.h"

Go to the source code of this file.

Functions
libMesh::ExplicitSystem &	add_explicit_elasticity (libMesh::EquationSystems &input_systems, libMesh::Order order=libMesh::FIRST, libMesh::FEFamily family=libMesh::LAGRANGE)
libMesh::ImplicitSystem &	add_elasticity (libMesh::EquationSystems &input_systems, libMesh::Order order=libMesh::FIRST, libMesh::FEFamily family=libMesh::LAGRANGE)
	Add a linear elasticity libMesh::LinearImplicitSystem to the input libMesh::EquationSystems& input_systems. More...
int	main (int argc, char **argv)

Detailed Description

Implementation of the parallel coupling matrices assembly.

Usage: ./CArl_assemble_coupling -i [input file]

This program uses the intersections previously constructed to build the couplig matrices. The input file is parsed by the carl::get_input_params(GetPot& field_parser, coupling_assemble_coupling_input_params& input_params) function, and it contains the following parameters.

Required parameters:

• System and intersection meshes:
  • MeshA, -mA or --meshA : path to the mesh A.
  • MeshB, -mB or --meshB : path to the mesh B.
  • InterBase, -mI or --meshI : common path to the intersection meshes and tables.
• Coupling parameters:
  • CouplingWidth or --ce : width of the coupling region (same unit as the meshes, in the coupling term).
  • CouplingRigidity or --ck : rigidity used for the coupling matrix (in MPa, if mm was used for the meshes, in both the and terms).

Optional parameters:

• Output:
  • OutputFolder or --output : base of the output folder. Default: "".
• Restriction meshes and tables:
  • Mesh_A_Restriction, -mAR or --meshAR : path to the restricted mesh A (formed by elements of the mesh A intersecting the coupling region). Default: [InterBase]_A_restriction.msh.
  • Mesh_B_Restriction, -mBR or --meshBR : path to the restricted mesh B (formed by elements of the mesh A intersecting the coupling region). Default: [InterBase]_B_restriction.msh.
    • Mesh_A_RestrictionEquivalenceTable or --tableRA : path to the equivalence table between the mesh A and its restriction. Default: [InterBase]_A_restriction_restrict.dat.
    • Mesh_B_RestrictionEquivalenceTable or --tableRB : path to the equivalence table between the mesh B and its restriction. Default: [InterBase]_B_restriction_restrict.dat.
• Mediator mesh:
  • MediatorMesh : choice of the mediator mesh. Values: UseRestricted_A or UseRestricted_B. Default: UseRestricted_A.

Definition in file CArl_assemble_coupling.cpp.

Function Documentation

libMesh::ImplicitSystem& add_elasticity	(	libMesh::EquationSystems &	input_systems,
		libMesh::Order	order = libMesh::FIRST,
		libMesh::FEFamily	family = libMesh::LAGRANGE
	)

Add a linear elasticity libMesh::LinearImplicitSystem to the input libMesh::EquationSystems& input_systems.

Definition at line 47 of file CArl_assemble_coupling.cpp.

{
    libMesh::ImplicitSystem& elasticity_system =
            input_systems.add_system<libMesh::ImplicitSystem> ("Elasticity");

    elasticity_system.add_variable("u", order, family);
    elasticity_system.add_variable("v", order, family);
    elasticity_system.add_variable("w", order, family);

    return elasticity_system;
}

libMesh::ExplicitSystem& add_explicit_elasticity	(	libMesh::EquationSystems &	input_systems,
		libMesh::Order	order = libMesh::FIRST,
		libMesh::FEFamily	family = libMesh::LAGRANGE
	)

Definition at line 33 of file CArl_assemble_coupling.cpp.

{
    libMesh::ExplicitSystem& elasticity_system =
            input_systems.add_system<libMesh::ExplicitSystem> ("Elasticity");

    elasticity_system.add_variable("u", order, family);
    elasticity_system.add_variable("v", order, family);
    elasticity_system.add_variable("w", order, family);

    return elasticity_system;
}

int main	(	int	argc,
		char **	argv
	)

Definition at line 61 of file CArl_assemble_coupling.cpp.

                                {

    // --- Initialize libMesh
    libMesh::LibMeshInit init(argc, argv);

    // Do performance log?
    const bool MASTER_bPerfLog_carl_libmesh = true;
    libMesh::PerfLog perf_log("Main program", MASTER_bPerfLog_carl_libmesh);

    // libMesh's C++ / MPI communicator wrapper
    libMesh::Parallel::Communicator& WorldComm = init.comm();

    // Number of processors and processor rank.
    int rank = WorldComm.rank();
    int nodes = WorldComm.size();

    // Create local communicator
    libMesh::Parallel::Communicator LocalComm;
    WorldComm.split(rank,rank,LocalComm);

    // --- Set up inputs

    // Command line parser
    GetPot command_line(argc, argv);

    // File parser
    GetPot field_parser;

    // If there is an input file, parse it to get the parameters. Else, parse the command line
    std::string input_filename;
    if (command_line.search(2, "--inputfile", "-i")) {
        input_filename = command_line.next(input_filename);
        field_parser.parse_input_file(input_filename, "#", "\n", " \t\n");
    } else {
        field_parser = command_line;
    }

    carl::coupling_assemble_coupling_input_params input_params;
    carl::get_assemble_coupling_input_params(field_parser, input_params);

    // Check libMesh installation dimension
    const unsigned int dim = 3;

    libmesh_example_requires(dim == LIBMESH_DIM, "3D support");

    // --- Set up the meshes

    // - Parallelized meshes: A, B, mediator and weight
    perf_log.push("Meshes - Parallel","Read files:");
    libMesh::Mesh mesh_BIG(WorldComm, dim);
    mesh_BIG.read(input_params.mesh_BIG_file);
    mesh_BIG.prepare_for_use();

    libMesh::Mesh mesh_micro(WorldComm, dim);
    mesh_micro.read(input_params.mesh_micro_file);
    mesh_micro.prepare_for_use();

    libMesh::Mesh mesh_mediator(WorldComm, dim);
    mesh_mediator.allow_renumbering(false);
    mesh_mediator.read(input_params.mesh_mediator_file);
    mesh_mediator.prepare_for_use();

    perf_log.pop("Meshes - Parallel","Read files:");

    // - Local meshes: restrict A and restrict B

    // -> libMesh's default mesh IS the ReplicatedMesh, which creates a copy of
    //    itself on each processor, but partitions the iterators over each
    //    processor to allow the parallelization of the code. The usage of
    //    ParallelMesh is still a bit risky, and, performance-wise, is worse
    //    than ReplicatedMesh for less than a few thousand processors.

    perf_log.push("Meshes - Serial","Read files:");
    libMesh::ReplicatedMesh mesh_R_BIG(WorldComm, dim);
    mesh_R_BIG.allow_renumbering(false);
    mesh_R_BIG.read(input_params.mesh_restrict_BIG_file);
    mesh_R_BIG.prepare_for_use();

    libMesh::ReplicatedMesh mesh_R_micro(WorldComm, dim);
    mesh_R_micro.allow_renumbering(false);
    mesh_R_micro.read(input_params.mesh_restrict_micro_file);
    mesh_R_micro.prepare_for_use();

    // - Local mesh: intersection mesh
    libMesh::Mesh mesh_inter(LocalComm, dim);
    mesh_inter.allow_renumbering(false);
    std::string local_inter_mesh_filename = input_params.common_inter_file + "_r_"
                                        + std::to_string(rank) + "_n_" + std::to_string(nodes) + ".e";
    std::string local_inter_table_filename = input_params.common_inter_file + "_r_"
                                        + std::to_string(rank) + "_n_" + std::to_string(nodes) + "_inter_table.dat";
    std::string global_inter_table_filename = input_params.common_inter_file + "_global_inter_pairs.dat";

    mesh_inter.read(local_inter_mesh_filename);
    mesh_inter.prepare_for_use();

    perf_log.pop("Meshes - Serial","Read files:");

    // --- Prepare the equivalence tables and the intersection mappings
    perf_log.push("Equivalence / intersection tables","Read files:");

    // Local intersection pairs (system meshes)
    std::unordered_map<int,std::pair<int,int> > local_intersection_pairs_map;

    // Local intersection pairs (restricted meshes)
    std::unordered_map<int,std::pair<int,int> > local_intersection_restricted_pairs_map;

    // Intersection elements to be treated by this processor
    std::unordered_map<int,int> local_intersection_meshI_to_inter_map;

    // Equivalence tables between system and restricted meshes (and vice-versa)
    std::unordered_map<int,int> equivalence_table_BIG_to_R_BIG;
    std::unordered_map<int,int> equivalence_table_micro_to_R_micro;
    std::unordered_map<int,int> equivalence_table_R_BIG_to_BIG;
    std::unordered_map<int,int> equivalence_table_R_micro_to_micro;

    //  Start by reading and broadcasting the equivalence tables
    carl::set_equivalence_tables(
            WorldComm,
            input_params.equivalence_table_restrict_BIG_file,
            input_params.equivalence_table_restrict_micro_file,

            equivalence_table_BIG_to_R_BIG,
            equivalence_table_micro_to_R_micro,
            equivalence_table_R_BIG_to_BIG,
            equivalence_table_R_micro_to_micro);

    // Set the local intersection tables
    if(input_params.mediator_type == carl::MediatorType::USE_MACRO)
    {
        carl::set_local_intersection_tables(
                WorldComm,
                mesh_inter,
                local_inter_table_filename,
                input_params.equivalence_table_restrict_BIG_file,
                input_params.equivalence_table_restrict_micro_file,

                equivalence_table_BIG_to_R_BIG,
                equivalence_table_micro_to_R_micro,

                local_intersection_pairs_map,
                local_intersection_restricted_pairs_map,
                local_intersection_meshI_to_inter_map);
    }
    else if(input_params.mediator_type == carl::MediatorType::USE_MICRO)
    {
        carl::set_local_intersection_tables(
                WorldComm,
                mesh_inter,
                local_inter_table_filename,
                input_params.equivalence_table_restrict_micro_file,
                input_params.equivalence_table_restrict_BIG_file,

                equivalence_table_micro_to_R_micro,
                equivalence_table_BIG_to_R_BIG,

                local_intersection_pairs_map,
                local_intersection_restricted_pairs_map,
                local_intersection_meshI_to_inter_map);
    }

    // Build mappings with the intersections of the mediator mesh with the micro and macro meshes - used to preallocate the coupling matrices
    std::unordered_multimap<int,int> inter_mediator_BIG;
    std::unordered_multimap<int,int> inter_mediator_micro;
    carl::set_global_mediator_system_intersection_lists(
            WorldComm,
            global_inter_table_filename,
            equivalence_table_BIG_to_R_BIG,
            equivalence_table_R_BIG_to_BIG,
            inter_mediator_BIG,
            inter_mediator_micro);
    perf_log.pop("Equivalence / intersection tables","Read files:");

    // --- Generate the equation systems
    perf_log.push("Initialization","System initialization:");
    carl::assemble_coupling_matrices CoupledMatrices(WorldComm);

    libMesh::EquationSystems& equation_systems_inter =
                    CoupledMatrices.add_inter_EquationSystem("InterSys", mesh_inter);

    libMesh::ExplicitSystem& elasticity_system_inter
                                        = add_explicit_elasticity(equation_systems_inter);

    carl::reduced_system_init(elasticity_system_inter);

    perf_log.pop("Initialization","System initialization:");

    // - Build the MACRO system

    perf_log.push("Macro system","System initialization:");
    libMesh::EquationSystems& equation_systems_BIG =
                    CoupledMatrices.set_BIG_EquationSystem("BigSys", mesh_BIG);

    // [MACRO] Set up the physical properties
    libMesh::ExplicitSystem& elasticity_system_BIG
                                        = add_explicit_elasticity(equation_systems_BIG);

    carl::reduced_system_init(elasticity_system_BIG);
    perf_log.pop("Macro system","System initialization:");

    // - Build the micro system

    perf_log.push("Micro system","System initialization:");
    libMesh::EquationSystems& equation_systems_micro =
                    CoupledMatrices.add_micro_EquationSystem<libMesh::PetscMatrix<libMesh::Number> >("MicroSys", mesh_micro);

    // [MICRO] Set up the physical properties
    libMesh::ExplicitSystem& elasticity_system_micro
                                        = add_explicit_elasticity(equation_systems_micro);

    carl::reduced_system_init(elasticity_system_micro);
    perf_log.pop("Micro system","System initialization:");

    // - Build the RESTRICTED BIG system
    perf_log.push("RESTRICTED macro system","System initialization:");
    libMesh::EquationSystems& equation_systems_R_BIG =
                    CoupledMatrices.set_Restricted_BIG_EquationSystem("BigSys", mesh_R_BIG);

    // [R. MACRO] Set up the physical properties
    libMesh::ExplicitSystem& elasticity_system_R_BIG
                                        = add_explicit_elasticity(equation_systems_R_BIG);

    carl::reduced_system_init(elasticity_system_R_BIG);

    perf_log.pop("RESTRICTED macro system","System initialization:");

    // - Build the RESTRICTED micro system

    perf_log.push("RESTRICTED micro system","System initialization:");
    libMesh::EquationSystems& equation_systems_R_micro =
                    CoupledMatrices.add_Restricted_micro_EquationSystem("MicroSys", mesh_R_micro);

    // [R. MICRO] Set up the physical properties
    libMesh::ExplicitSystem& elasticity_system_R_micro
                                        = add_explicit_elasticity(equation_systems_R_micro);

    carl::reduced_system_init(elasticity_system_R_micro);
    perf_log.pop("RESTRICTED micro system","System initialization:");

    // - Build the mediator system

    perf_log.push("Mediator system","System initialization:");
    libMesh::EquationSystems& equation_systems_mediator =
                    CoupledMatrices.add_mediator_EquationSystem("MediatorSys", mesh_mediator);

    libMesh::ExplicitSystem& elasticity_system_mediator
                                        = add_explicit_elasticity(equation_systems_mediator);

    carl::reduced_system_init(elasticity_system_mediator);

    perf_log.pop("Mediator system","System initialization:");

    // Set parameters
    CoupledMatrices.set_coupling_parameters("MicroSys",input_params.coupling_rigidity,input_params.coupling_width);

    // Use H1 norm
    CoupledMatrices.use_H1_coupling("MicroSys");

    // Assemble!
    CoupledMatrices.assemble_coupling_elasticity_3D_parallel("BigSys","MicroSys",
            "InterSys","MediatorSys",
            mesh_R_BIG, mesh_R_micro,
            local_intersection_pairs_map,
            local_intersection_restricted_pairs_map,
            local_intersection_meshI_to_inter_map,
            inter_mediator_BIG,
            inter_mediator_micro);

    // Print matrices!
    if(rank == 0)
    {
        std::string command_string = "mkdir -p " + input_params.output_folder;
        carl::exec_command(command_string.c_str());
    }
    WorldComm.barrier();

// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
    CoupledMatrices.print_matrices_matlab("MicroSys",input_params.output_folder);
#endif
    CoupledMatrices.print_PETSC_matrices("MicroSys",input_params.output_folder);

    return 0;
}