yohai/phigrape
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Improved HDF5 reader and added ASCII writer with custom precision

Browse source
This commit is contained in:
Yohai Meiron 2020-03-28 01:34:37 -04:00
parent ba5546534f
commit b2943be7c1
1 changed files with 33 additions and 15 deletions
Download patch file Download diff file Expand all files Collapse all files

48
io.cpp
View file

@ -1,4 +1,5 @@
#include "hdf5.h" #include "hdf5.h"
#include <cmath>
#include <string> #include <string>
#include <vector> #include <vector>
#include <algorithm> #include <algorithm>
@ -6,6 +7,18 @@
struct double3 {double x,y,z; struct double3 {double x,y,z;
}; };
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)
{
int id_width = (int)log10(N-1) + 1;
char string_template[256];
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);
printf("%d\n", step_num);
printf("%d\n", N);
printf("%.16E\n", t);
for (int i=0; i<N; i++) {
printf(string_template, i, m[i], x[i].x, x[i].y, x[i].z, v[i].x, v[i].y, v[i].z);
}
}
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) 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)
{ {
@ -70,13 +83,17 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
*step_num = *max_element(step_num_arr.begin(), step_num_arr.end()); *step_num = *max_element(step_num_arr.begin(), step_num_arr.end());
// Prepare to read the data sets dimensionality data. // Prepare to read the data sets dimensionality data.
char dataset_path[256]; char path[256];
hid_t dataset_id, dataspace_id; hid_t attr_id, dataset_id, dataspace_id;
int ndims; int ndims;
hsize_t dims[2]; hsize_t dims[2];
sprintf(dataset_path, "/Step#%d/MASS", *step_num); sprintf(path, "/Step#%d", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT); attr_id = H5Aopen_by_name(file_id, path, "Time", H5P_DEFAULT, H5P_DEFAULT);
H5Aread(attr_id, H5T_NATIVE_DOUBLE, t);
sprintf(path, "/Step#%d/MASS", *step_num);
dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id); dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id); ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 1) if (ndims != 1)
@ -85,24 +102,22 @@ void h5_read(const std::string file_name, int *step_num, int *N, double *t, doub
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m); H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m);
*N = dims[0]; *N = dims[0];
sprintf(dataset_path, "/Step#%d/X", *step_num); sprintf(path, "/Step#%d/X", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT); dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id); dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id); ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 2) throw std::runtime_error("Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 2-dimensional)"); if (ndims != 2) throw std::runtime_error("Bad dimensionality");
H5Sget_simple_extent_dims(dataspace_id, dims, NULL); H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
if (dims[0] != *N) throw std::runtime_error("Expected " + std::to_string(*N) + "rows in Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " (based on MASS)"); if ((dims[0] != *N) || (dims[1] != 3)) throw std::runtime_error("Bad dimensionality");
if (dims[1] != 3) throw std::runtime_error("Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " has " + std::to_string(dims[1]) + " columns (expected 3 columns)");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)x); H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)x);
sprintf(dataset_path, "/Step#%d/V", *step_num); sprintf(path, "/Step#%d/V", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT); dataset_id = H5Dopen2(file_id, path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id); dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id); ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 2) throw std::runtime_error("Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 2-dimensional)"); if (ndims != 2) throw std::runtime_error("Bad dimensionality");
H5Sget_simple_extent_dims(dataspace_id, dims, NULL); H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
if (dims[0] != *N) throw std::runtime_error("Expected " + std::to_string(*N) + "rows in Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " (based on MASS)"); if ((dims[0] != *N) || (dims[1] != 3)) throw std::runtime_error("Bad dimensionality");
if (dims[1] != 3) throw std::runtime_error("Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " has " + std::to_string(dims[1]) + " columns (expected 3 columns)");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)v); H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)v);
} }
@ -127,7 +142,10 @@ int main()
h5_write("123.h5", 17, N, 123.987, (double*)x, x, x, (double*)x, x, x, 7, true); h5_write("123.h5", 17, N, 123.987, (double*)x, x, x, (double*)x, x, x, 7, true);
h5_read("123.h5", &step_num, &N, &t, m, x, v); h5_read("123.h5", &step_num, &N, &t, m, x, v);
printf("%d %d %f\n", step_num, N, t); printf("%d %d %f\n", step_num, N, t);
#error still havent implemented reading the time attribute
ascii_write("123.dat", 0, N, t, m, x, v, 10);
// h5_write(file_name, 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7); // h5_write(file_name, 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7);