src/HDF5Reader.cpp

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#include "HDF5Reader.h"
using namespace std;

HDF5Reader::~HDF5Reader() {
//File closing operations here
    cout << "Close file: "; 
    _status = H5Fclose(_file);
    assert (_status >= 0);
    cout << "OK" << endl;
}

HDF5Reader::HDF5Reader(const char* inputFile, MeshBuilder* builder)
    : _builder(builder), _inputFile(inputFile), _dataset(0) {

// Open HDF5 file here
    _file = H5Fopen(_inputFile, H5F_ACC_RDONLY, H5P_DEFAULT);
    assert(_file  >= 0);
    if (_file < 0)
        throw FileIOError(_inputFile, "error opening file");
    

}
void HDF5Reader::read() {

//Read number of nodes
    _dataset = H5Dopen(_file, "/coords");
    hid_t x = H5Dget_space(_dataset);
    H5Sget_simple_extent_dims(x, _dimsf, NULL);
    _nof_node = _dimsf[0];
    _builder->init_coord(_nof_node); //initialize builder with number of nodes

//Read node coordinates
    double* nodes = new double[_dimsf[0] * _dimsf[1]];
    _status = H5Dread(_dataset, REALMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &nodes[0]);
    assert (_status >=0);

    for (int i = 0; i < _nof_node; i ++) {
        _builder->set_coord(i, nodes[3 * i], nodes[3 * i + 1], nodes[3 * i + 2]);
    }

    delete nodes;
    _builder->finalize_coord();

//Read number of tets
    _dataset = H5Dopen(_file, "/tetids");
    x = H5Dget_space(_dataset);
    H5Sget_simple_extent_dims(x, _dimsf, NULL);
    int nof_tets = _dimsf[0];
    _builder->init_coord(nof_tets);

//Read tetnodes and materials
    int* tetids = new int[_dimsf[0] * _dimsf[1]];
    _status = H5Dread(_dataset, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &tetids[0]);
    assert (_status >=0);

//Read number of materials
    _dataset = H5Dopen(_file, "/matids");
    x = H5Dget_space(_dataset);
    H5Sget_simple_extent_dims(x, _dimsf, NULL);

    //Read tetnodes and materials
    int* matids = new int[_dimsf[0]];
    _status = H5Dread(_dataset, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &matids[0]);
    assert (_status >=0);

    for (int i = 0; i < nof_tets; i ++) {
      _builder->set_tet(i, tetids[4 * i], tetids[4 * i + 1], tetids[4 * i + 2], tetids[4 * i + 3], matids[i]);
    }

    delete tetids;
    delete matids;
    _builder->finalize_tet();

//Read number of boundary faces
    _dataset = H5Dopen(_file, "/surface");
    x = H5Dget_space(_dataset);
    H5Sget_simple_extent_dims(x, _dimsf, NULL);
    int nof_bc_face = _dimsf[0];
    _builder->init_coord(nof_bc_face);

//Read boundary face data
    int* faceids = new int[_dimsf[0] * _dimsf[1]];
    _status = H5Dread(_dataset, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &faceids[0]);
    assert (_status >=0);

    int nof_bc[4] = {0, 0, 0, 0};
    for (int i = 0; i < nof_bc_face; i ++) {
        nof_bc[faceids[4 * i]] += 1;
        _builder->set_bc(faceids[4 * i + 1], faceids[4 * i + 2], faceids[4 * i + 3], faceids[4 * i]);
    }
    
//Symmetry planes
    int nof_sym;
    for (nof_sym = 3; nof_sym >= 0 && nof_bc[nof_sym] == 0; nof_sym --);
    
    assert(nof_sym >= 0);
    for (int i = 1; i < nof_sym; i ++)
        if(nof_bc[i] == 0)
            throw FileIOError(_inputFile, "empty symmetry plane detected");
            
    delete faceids;
    _builder->finalize_bc(nof_sym);

}

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