Completed HDF5 support
This commit is contained in:
Yohai Meiron
parent
b2943be7c1
commit
5cb4282be4
8 changed files with 258 additions and 185 deletions
202
io.cpp
202
io.cpp
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@ -1,71 +1,79 @@
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#ifdef HAS_HDF5
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#include "hdf5.h"
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#endif
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#include "double3.h"
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#include <fstream>
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#include <cstring>
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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 <string>
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#include <stdexcept>
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struct double3 {double x,y,z;
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};
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bool is_hdf5(std::string file_name)
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{
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std::ifstream file(file_name, std::ifstream::binary);
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const char hdf5_magic[] = "\x89HDF\x0d\x0a\x1a\x0a";
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char buffer[8];
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file.read(buffer, 8);
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if (!file) throw std::runtime_error("Unable to read file " + file_name);
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bool result = (memcmp(buffer, hdf5_magic, 8)==0);
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file.close();
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return result;
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}
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void ascii_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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char rest[512];
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int result;
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std::ifstream file(file_name);
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if (!file.good()) throw std::runtime_error("File " + file_name + " not found.");
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std::string str;
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std::getline(file, str);
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result = sscanf(str.c_str(), "%d%s", step_num, rest);
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if (result!=1) throw std::runtime_error("Error parsing line 1: expected one integer");
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std::getline(file, str);
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result = sscanf(str.c_str(), "%d%s", N, rest);
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if (result!=1) throw std::runtime_error("Error parsing line 2: expected one integer");
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std::getline(file, str);
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result = sscanf(str.c_str(), "%lf%s", t, rest);
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if (result!=1) throw std::runtime_error("Error parsing line 3: expected one real number");
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int i = -1;
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while (std::getline(file, str)) {
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if (++i > *N) throw std::runtime_error("Error parsing line " + std::to_string(i+4) + ": particle out of range");
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result = sscanf(str.c_str(), "%*s %lf %lf %lf %lf %lf %lf %lf%s", &m[i], &x[i][0], &x[i][1], &x[i][2], &v[i][0], &v[i][1], &v[i][2], rest);
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}
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file.close();
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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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auto file = std::ofstream(file_name);
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if (!file.is_open()) throw std::runtime_error("Cannot open file for output");
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int id_width = (int)log10(N-1) + 1;
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char string_template[256];
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char string_template[256], output_string[256];
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file << step_num << '\n';
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file << N << '\n';
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file.precision(16);
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file << std::scientific << t << '\n';
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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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sprintf(output_string, string_template, i, m[i], x[i][0], x[i][1], x[i][2], v[i][0], v[i][1], v[i][2]);
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file << output_string;
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}
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file.close();
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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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#ifdef HAS_HDF5
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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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@ -91,6 +99,7 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
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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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H5Aclose(attr_id);
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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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@ -100,6 +109,8 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
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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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H5Sclose(dataspace_id);
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H5Dclose(dataset_id);
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*N = dims[0];
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sprintf(path, "/Step#%d/X", *step_num);
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@ -110,6 +121,8 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
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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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H5Sclose(dataspace_id);
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H5Dclose(dataset_id);
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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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@ -119,36 +132,65 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
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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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H5Sclose(dataspace_id);
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H5Dclose(dataset_id);
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H5Gclose(group_id);
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H5Fclose(file_id);
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#else
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throw std::runtime_error("h5_read was called but compiled without HDF5 support");
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#endif
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}
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int main()
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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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// 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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#ifdef HAS_HDF5
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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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// 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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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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// static int zzz = 5;
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file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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// file_id = H5Fcreate(std::to_string(zzz).c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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// zzz++;
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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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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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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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H5close(); // If we don't do that (HDF5 1.10.5) then the file isn't really closed...
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#else
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throw std::runtime_error("h5_write was called but compiled without HDF5 support");
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#endif
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}
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