154 lines
6.3 KiB
C++
154 lines
6.3 KiB
C++
#include "hdf5.h"
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#include <cmath>
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#include <string>
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#include <vector>
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#include <algorithm>
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#include <stdexcept>
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struct double3 {double x,y,z;
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};
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void ascii_write(const std::string file_name, const int step_num, const int N, const double t, const double *m, const double3 *x, const double3 *v, int precision=10)
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{
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int id_width = (int)log10(N-1) + 1;
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char string_template[256];
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sprintf(string_template, "%%0%dd%%%d.%dE%%%d.%dE%%%d.%dE%%%d.%dE%%%d.%dE%%%d.%dE%%%d.%dE\n", id_width, precision+7, precision, precision+8, precision, precision+8, precision, precision+8, precision, precision+8, precision, precision+8, precision, precision+8, precision);
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printf("%d\n", step_num);
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printf("%d\n", N);
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printf("%.16E\n", t);
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for (int i=0; i<N; i++) {
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printf(string_template, i, m[i], x[i].x, x[i].y, x[i].z, v[i].x, v[i].y, v[i].z);
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}
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}
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void h5_write(const std::string file_name, const int step_num, const int N, const double t, 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)
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{
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bool write_pot = (write_mode )%2;
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bool write_acc = (write_mode>>1)%2;
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bool write_jrk = (write_mode>>2)%2;
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hid_t file_id, group_id, attribute_id, dataset_id, dataspace_id;
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hsize_t dims[2] = {(hsize_t)N, 3};
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hid_t h5_float_type;
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if (use_double_precision) h5_float_type = H5T_IEEE_F64LE;
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else h5_float_type = H5T_IEEE_F32LE;
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file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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char group_name[32];
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sprintf(group_name, "/Step#%d", step_num);
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group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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dataspace_id = H5Screate(H5S_SCALAR);
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attribute_id = H5Acreate2 (group_id, "Time", H5T_IEEE_F64LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
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H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &t);
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H5Sclose(dataspace_id);
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auto write_dataset = [&](const char dataset_name[], int ndims, double *data) {
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hid_t dataspace_id = H5Screate_simple(ndims, dims, NULL);
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char dataset_path[32];
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sprintf(dataset_path, "%s/%s", group_name, dataset_name);
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hid_t dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
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H5Dclose(dataset_id);
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H5Sclose(dataspace_id);
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};
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write_dataset("MASS", 1, (double*)m);
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write_dataset("X", 2, (double*)x);
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write_dataset("V", 2, (double*)v);
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if (write_pot) write_dataset("POT", 1, (double*)pot);
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if (write_acc) write_dataset("ACC", 2, (double*)acc);
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if (write_jrk) write_dataset("JRK", 2, (double*)jrk);
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H5Gclose(group_id);
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H5Fclose(file_id);
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}
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void h5_read(const std::string file_name, int *step_num, int *N, double *t, double m[], double3 x[], double3 v[])
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{
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// Open file and root group; count number of top level objects
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hid_t file_id = H5Fopen(file_name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
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hid_t group_id = H5Gopen2(file_id, "/", H5P_DEFAULT);
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H5G_info_t object_info;
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H5Gget_info(group_id, &object_info);
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// Iterate over objects and add the number of each "step" group into a vector
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std::vector<int> step_num_arr;
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for (int i=0; i<object_info.nlinks; i++) {
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char name_cstr[256];
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H5Gget_objname_by_idx(group_id, i, name_cstr, 256);
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std::string name(name_cstr);
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if (name.substr(0, 5) == "Step#") step_num_arr.push_back(std::stoi(name.substr(5, std::string::npos)));
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}
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// Find the highest step in the file
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*step_num = *max_element(step_num_arr.begin(), step_num_arr.end());
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// Prepare to read the data sets dimensionality data.
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char path[256];
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hid_t attr_id, dataset_id, dataspace_id;
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int ndims;
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hsize_t dims[2];
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sprintf(path, "/Step#%d", *step_num);
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attr_id = H5Aopen_by_name(file_id, path, "Time", H5P_DEFAULT, H5P_DEFAULT);
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H5Aread(attr_id, H5T_NATIVE_DOUBLE, t);
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sprintf(path, "/Step#%d/MASS", *step_num);
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dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
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dataspace_id = H5Dget_space(dataset_id);
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ndims = H5Sget_simple_extent_ndims(dataspace_id);
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if (ndims != 1)
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throw std::runtime_error("Dataset MASS in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 1-dimensional)");
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H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
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H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m);
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*N = dims[0];
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sprintf(path, "/Step#%d/X", *step_num);
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dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
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dataspace_id = H5Dget_space(dataset_id);
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ndims = H5Sget_simple_extent_ndims(dataspace_id);
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if (ndims != 2) throw std::runtime_error("Bad dimensionality");
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H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
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if ((dims[0] != *N) || (dims[1] != 3)) throw std::runtime_error("Bad dimensionality");
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H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)x);
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sprintf(path, "/Step#%d/V", *step_num);
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dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
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dataspace_id = H5Dget_space(dataset_id);
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ndims = H5Sget_simple_extent_ndims(dataspace_id);
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if (ndims != 2) throw std::runtime_error("Bad dimensionality");
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H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
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if ((dims[0] != *N) || (dims[1] != 3)) throw std::runtime_error("Bad dimensionality");
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H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)v);
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}
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int main()
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{
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// double3 aaa;
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// double pot;
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std::string file_name = "new_file.h5";
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int N = 25;
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double3 x[N];
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for (int i=0; i<N; i++) {
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x[i].x=i+0.01;
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x[i].y=i+0.02;
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x[i].z=i+0.03;
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}
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double m[N];
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double3 v[N];
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int step_num;
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double t;
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h5_write("123.h5", 17, N, 123.987, (double*)x, x, x, (double*)x, x, x, 7, true);
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h5_read("123.h5", &step_num, &N, &t, m, x, v);
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printf("%d %d %f\n", step_num, N, t);
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ascii_write("123.dat", 0, N, t, m, x, v, 10);
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// h5_write(file_name, 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7);
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// h5_read(file_name, &N, (double*)x, x, x);
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// printf("aaaa %d %d %d\n", ndims, dims[0], dims[1]);
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}
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