phigrape/io.cpp

#include "hdf5.h"
#include <string>
#include <vector>
#include <algorithm>
struct double3 {double x,y,z;};

void h5_write(const std::string file_name, const int step_num, const double t, const int N, const double *m, const double3 *x, const double3 *v, const double *pot, const double3 *acc, const double3 *jrk, const int write_mode=0, const bool use_double_precision=true)
{
    char group_name[32], dataset_path[32];
    bool write_pot = (write_mode   )%2;
    bool write_acc = (write_mode>>1)%2;
    bool write_jrk = (write_mode>>2)%2;

    hid_t file_id, group_id, attribute_id, dataset_id, dataspace_id;
    hsize_t dims[2] = {(hsize_t)N, 3};

    hid_t h5_float_type;
    if (use_double_precision) h5_float_type = H5T_IEEE_F64LE;
    else h5_float_type = H5T_IEEE_F32LE;

    file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
    sprintf(group_name, "/Step#%d", step_num);
    group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    dataspace_id = H5Screate(H5S_SCALAR);
    attribute_id = H5Acreate2 (group_id, "Time", H5T_IEEE_F64LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
    H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &t);
    H5Sclose(dataspace_id);

    dataspace_id = H5Screate_simple(1, dims, NULL);
    sprintf(dataset_path, "%s/MASS", group_name);
    dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m);
    H5Dclose(dataset_id);
    H5Sclose(dataspace_id);

    dataspace_id = H5Screate_simple(2, dims, NULL);
    sprintf(dataset_path, "%s/X", group_name);
    dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
    H5Dclose(dataset_id);
    H5Sclose(dataspace_id);

    dataspace_id = H5Screate_simple(2, dims, NULL);
    sprintf(dataset_path, "%s/V", group_name);
    dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, v);
    H5Dclose(dataset_id);
    H5Sclose(dataspace_id);

    if (write_pot) {
        dataspace_id = H5Screate_simple(1, dims, NULL);
        sprintf(dataset_path, "%s/POT", group_name);
        dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, pot);
        H5Dclose(dataset_id);
        H5Sclose(dataspace_id);
    }
    if (write_acc) {
        dataspace_id = H5Screate_simple(2, dims, NULL);
        sprintf(dataset_path, "%s/ACC", group_name);
        dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, acc);
        H5Dclose(dataset_id);
        H5Sclose(dataspace_id);
    }
    if (write_jrk) {
        dataspace_id = H5Screate_simple(2, dims, NULL);
        sprintf(dataset_path, "%s/JRK", group_name);
        dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, jrk);
        H5Dclose(dataset_id);
        H5Sclose(dataspace_id);
    }
    H5Gclose(group_id);

    
    group_id = H5Gcreate2(file_id, "/Step#22", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    H5Gclose(group_id);
    
    
    H5Fclose(file_id);
}




herr_t file_info(hid_t loc_id, const char *name, void *opdata)
{
    H5G_stat_t statbuf;

    /*
     * Get type of the object and display its name and type.
     * The name of the object is passed to this function by 
     * the Library. Some magic :-)
     */
    H5Gget_objinfo(loc_id, name, 0, &statbuf);
    switch (statbuf.type) {
    case H5G_GROUP: 
         printf(" Object with name %s is a group \n", name);
         break;
    case H5G_DATASET: 
         printf(" Object with name %s is a dataset \n", name);
         break;
    case H5G_TYPE: 
         printf(" Object with name %s is a named datatype \n", name);
         break;
    default:
         printf(" Unable to identify an object ");
    }
    return 0;
 }




int main()
{
//     double3 aaa;
//     double pot;
    int N = 25;
    double3 x[N];
    for (int i=0; i<N; i++) {
        x[i].x=i+0.01;
        x[i].y=i+0.02;
        x[i].z=i+0.03;
    }
    h5_write("new_file.h5", 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7);
    
    auto file_id = H5Fopen("new_file.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
    auto group_id = H5Gopen2(file_id, "/", H5P_DEFAULT);
    H5G_info_t object_info;
    H5Gget_info(group_id, &object_info);
    std::vector<int> step_num;
    for (int i=0; i<object_info.nlinks; i++) {
        char name_cstr[256];
        H5Gget_objname_by_idx(group_id, i, name_cstr, 256);
        std::string name(name_cstr);
        if (name.substr(0, 5) == "Step#") step_num.push_back(std::stoi(name.substr(5, std::string::npos)));
    }
    int step_num_max = *max_element(step_num.begin(), step_num.end());
    
    
    char dataset_path[256];
    sprintf(dataset_path, "/Step#%d/X", step_num_max);
    
    
    double dset_data[1024*1024];
    
    auto dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT);
    H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data);
    
    
//     printf("aaaa %d\n", step_num_max);
}