src/HDF5FileBuilder.cpp

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#include <new>
#include <iostream>
#include "HDF5FileBuilder.h"

using namespace std;

HDF5FileBuilder::HDF5FileBuilder(const char* outputFile)
    : _bc_face_counter(0) {

    // Open HDF5 file here
    cout << "Create file '" << outputFile << "': ";
    file = H5Fcreate(outputFile, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    assert (file >= 0);    
    cout << "OK" << endl;
}

// File closing operations here
HDF5FileBuilder::~HDF5FileBuilder() {
    cout << "Close file: "; 
    status = H5Fclose(file);
    assert (status >= 0);
    cout << "OK" << endl;
}

// Set on row in node coordinate matrix
void HDF5FileBuilder::set_coord(int i, double x, double y, double z) {
    _coord[3*i + 0] = x;
    _coord[3*i + 1] = y;
    _coord[3*i + 2] = z;
}

// Initialize the node matrix as an mx3 matrix
void HDF5FileBuilder::init_coord(int nof_node) {
    //allocate buffer 'n that's it.
    _nof_node = nof_node;
    _coord = new double[3*nof_node];    
}

// Flush node coordinate buffer 
void HDF5FileBuilder::finalize_coord() {

    cout << ".Create node coordinate dataspace: ";
    dimsf[0]=_nof_node;
    dimsf[1]=3;
    pointspace = H5Screate_simple(2, dimsf, NULL); 
    assert (pointspace >= 0);
    cout << "OK" << endl;

    // Creating the dataset within the dataspace                      
    cout << "..Create coordinate dataset: ";
    points = H5Dcreate(file, "coords", REALFILETYPE, pointspace, H5P_DEFAULT);
    assert (points >= 0);
    cout << "OK" << endl;
    
    cout << "..Writing dataset to dataspace: ";
    status = H5Dwrite(points, REALMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &_coord[0]);
    assert (status >= 0);
    cout << "OK" << endl;

    // Close the dataspaces and dataset
    cout << ".Close dataspace and dataset: ";
    status = H5Sclose(pointspace);
    assert (status >= 0);
    status = H5Dclose(points);
    assert (status >= 0);
    cout << "OK" << endl;

    // Free memory
    delete _coord;
}

//initialize tetrahedra mesh matrix
void HDF5FileBuilder::init_tet(int nof_tet) {
   //allocate buffer 'n that's it.
    _nof_tet = nof_tet;
    _tet_node = new int[4*_nof_tet];    
    _material = new int[_nof_tet];    
}

//Set one row of matrix of node ids of nodes forming tetrahedron t 
void HDF5FileBuilder::set_tet(int t, int id0, int id1, int id2, int id3, int material) {
    _tet_node[4*t + 0] = id0;
    _tet_node[4*t + 1] = id1;
    _tet_node[4*t + 2] = id2;
    _tet_node[4*t + 3] = id3;
    _material[t] = material;
}

// Flush terahedra buffer
void HDF5FileBuilder::finalize_tet() {
    cout << ".Create tetrahedra nodes dataspace: ";
    dimsf[0]=_nof_tet;
    dimsf[1]=4;
    tetspace = H5Screate_simple(2, dimsf, NULL); 
    assert (tetspace >= 0);
    cout << "OK" << endl;

    // Creating the dataset within the dataspace                      
    cout << "..Create dataset: ";
    tets = H5Dcreate(file, "tetids", INTFILETYPE, tetspace, H5P_DEFAULT);
    assert (tets >= 0);
    cout << "OK" << endl;

    cout << "..Writing dataset to dataspace: ";
    status = H5Dwrite(tets, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &_tet_node[0]);
    assert (status >= 0);
    cout << "OK" << endl;

    // Close the dataspaces and dataset
    cout << ".Close dataspace and dataset: ";
    status = H5Sclose(tetspace);
    assert (status >= 0);
    status = H5Dclose(tets);
    assert (status >= 0);
    cout << "OK" << endl;

    // Free memory
    delete _tet_node;


    // 
    // OSCAR: Add the material indices stored in _material
    //
    cout << ".Create materials dataspace: ";
    dimsf[0]=_nof_tet;
    dimsf[1]=1;
    matspace = H5Screate_simple(2, dimsf, NULL); 
    assert (matspace >= 0);
    cout << "OK" << endl;

    // Creating the dataset within the dataspace                      
    cout << "..Create dataset: ";
    mats = H5Dcreate(file, "matids", INTFILETYPE, matspace, H5P_DEFAULT);
    assert (mats >= 0);
    cout << "OK" << endl;

    cout << "..Writing dataset to dataspace: ";
    status = H5Dwrite(mats, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &_material[0]);
    assert (status >= 0);
    cout << "OK" << endl;

    // Close the dataspaces and dataset
    cout << ".Close dataspace and dataset: ";
    status = H5Sclose(matspace);
    assert (status >= 0);
    status = H5Dclose(mats);
    assert (status >= 0);
    cout << "OK" << endl;

    // Free memory
    delete _material;
   
}

//Initialize boundary face matrix
void HDF5FileBuilder::init_bc(int nof_bc_face) {
   //allocate buffer 'n that's it.
    _nof_bc_face = nof_bc_face;
    _bc_face = new int[4*_nof_bc_face];    

    _bc_face_counter = 0; //Face iterator set to zero
}

//Set one row of boundary condition bc_id to boundary triangle formed of nodes id0, id1 and id2.
void HDF5FileBuilder::set_bc(int id0, int id1, int id2, int bc_id) {

    _bc_face[4*_bc_face_counter + 0] = bc_id;
    _bc_face[4*_bc_face_counter + 1] = id0;
    _bc_face[4*_bc_face_counter + 2] = id1;
    _bc_face[4*_bc_face_counter + 3] = id2;

    _bc_face_counter++;
}

void HDF5FileBuilder::finalize_bc(int nof_sym) {
    cout << ".Create boundary/symmetry face dataspace: ";
    dimsf[0]=_nof_bc_face;
    dimsf[1]=4;
    edgespace = H5Screate_simple(2, dimsf, NULL); 
    assert (edgespace >= 0);
    cout << "OK" << endl;

    // Creating the dataset within the dataspace                      
    cout << "..Create dataset: ";
    edges = H5Dcreate(file, "surface", INTFILETYPE, edgespace, H5P_DEFAULT);
    assert (edges >= 0);
    cout << "OK" << endl;

    cout << "..Writing dataset to dataspace: ";
    status = H5Dwrite(edges, INTMEMTYPE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &_bc_face[0]);
    assert (status >= 0);
    cout << "OK" << endl;

    // Close the dataspaces and dataset
    cout << ".Close dataspace and dataset: ";
    status = H5Sclose(edgespace);
    assert (status >= 0);
    status = H5Dclose(edges);
    assert (status >= 0);
    cout << "OK" << endl;

    // Free memory
    delete _bc_face;
}

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