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h5_io.c
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h5_io.c
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#include "hdf5.h"
#include <stdlib.h>
#include <string.h>
/*
_
|_| |_ | | _|_ o | _
| | _) |_| |_ | | _>
*/
void strcati(char *foobar, char *foo, char *bar) {
// Concat foo and bar and copying it foobar"
// Assume foobar is large enought"
memset(foobar, 0, strlen(foobar));
strcpy(foobar, foo);
strcat(foobar, bar);
}
void H5Dread666(hid_t file_id, char *h, char *path, hid_t H5T_USER, void *data) {
herr_t status;
hid_t dataset_id;
char str[80];
strcati(str, h, path);
printf("h5: Reading %s \n", str);
dataset_id = H5Dopen(file_id, str, H5P_DEFAULT);
status = H5Dread(dataset_id, H5T_USER, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
status = H5Dclose(dataset_id);
}
void H5Dread666_hyperslab(hid_t file_id, char *h, char *path, hsize_t *start, hsize_t *count, hid_t memspace, hid_t H5T_USER, void *data) {
char str[80];
hid_t dataset_id; /* identifiers */
hid_t dataspace_id; /* identifiers */
herr_t status;
memspace = H5Screate_simple(1, count, NULL);
strcati(str, h, path);
printf("h5: Reading %s from %i to %i \n", str, start[0], start[0]+count[0]);
dataset_id = H5Dopen(file_id, str, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
status = H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Dread(dataset_id, H5T_USER, memspace, dataspace_id, H5P_DEFAULT, data);
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
}
void H5Dcreate666(hid_t file_id, char *h, char *path, hsize_t *dims, int dims_size, hid_t H5T_USER) {
herr_t status;
hid_t dataspace_id, dataset_id;
dataspace_id = H5Screate_simple(dims_size, dims, NULL);
char str[80];
strcati(str, h, path);
printf("h5: Creating %s \n", str);
dataset_id = H5Dcreate2(file_id, str, H5T_USER, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
}
void H5Dcreate_scalar666w(hid_t file_id, char *h, char *path, hid_t H5T_USER, void *data) {
herr_t status;
hid_t dataspace_id, dataset_id;
dataspace_id = H5Screate(H5S_SCALAR);
char str[80];
strcati(str, h, path);
printf("h5: Creating and writting scalar %s \n", str);
dataset_id = H5Dcreate2(file_id, str, H5T_USER, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_USER, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
status = H5Dclose(dataset_id);
status = H5Sclose(dataspace_id);
}
void H5Dwrite666(hid_t file_id, char *h, char *path, hid_t H5T_USER, void *data) {
herr_t status;
hid_t dataset_id;
char str[80];
strcati(str, h, path);
printf("h5: Writing %s \n", str);
dataset_id = H5Dopen(file_id, str, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_USER, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
status = H5Dclose(dataset_id);
}
/*
_ _
|_) _ _. _| _|_ ._ _ _|_ o _ ._
| \ (/_ (_| (_| | |_| | | (_ |_ | (_) | |
*/
void get_param_h5_int_(char *h5path, int *n_bielec, int *n_hcore, int *flag) {
char *h = (flag[0] == 0) ? "mo" : "ao";
hid_t file_id;
herr_t status;
file_id = H5Fopen(h5path, H5F_ACC_RDONLY, H5P_DEFAULT);
H5Dread666(file_id, h, "/ints/two_e/n", H5T_NATIVE_INT, n_bielec);
H5Dread666(file_id, h, "/ints/one_e/hcore/n", H5T_NATIVE_INT, n_hcore);
status = H5Fclose(file_id);
}
void read_bielec_h5_(char *h5path, int32_t *bielec_idx, double *bielec_val, int *offset, int *chunk_size, int *flag) {
char *h = (flag[0] == 0) ? "mo" : "ao";
hid_t file_id; /* identifiers */
herr_t status;
hid_t memspace;
file_id = H5Fopen(h5path, H5F_ACC_RDONLY, H5P_DEFAULT);
hsize_t start[1] = {offset[0]};
hsize_t count[1] = {chunk_size[0]};
memspace = H5Screate_simple(1, count, NULL);
H5Dread666_hyperslab(file_id, h, "/ints/two_e/value", start, count, memspace, H5T_NATIVE_DOUBLE, bielec_val);
H5Dread666_hyperslab(file_id, h, "/ints/two_e/idx", start, count, memspace, H5T_NATIVE_LLONG, bielec_idx);
status = H5Fclose(file_id);
}
void read_hcore_h5_(char *h5path, int32_t *bielec_idx, double *bielec_val, int *flag) {
char *h = (flag[0] == 0) ? "mo" : "ao";
hid_t file_id; /* identifiers */
herr_t status;
file_id = H5Fopen(h5path, H5F_ACC_RDONLY, H5P_DEFAULT);
H5Dread666(file_id, h, "/ints/one_e/hcore/value", H5T_NATIVE_DOUBLE, bielec_val);
H5Dread666(file_id, h, "/ints/one_e/hcore/idx", H5T_NATIVE_LLONG, bielec_idx);
status = H5Fclose(file_id);
}
/*
_
\ / ._ o _|_ _ _|_ ._ _ _|_ o _ ._
\/\/ | | |_ (/_ | |_| | | (_ |_ | (_) | |
*/
void write_init_h5_(char *h5path, int *o_tot_num, int *bi_elec_num, int *flag, double *nr) {
herr_t status;
hid_t dataset_id;
hsize_t dims[2];
hid_t file_id = H5Fcreate(h5path, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// =~=~=~=
// H_core
// =~=~=~=
hid_t grp_crt_plist = H5Pcreate(H5P_LINK_CREATE);
/* Set flag for intermediate group creation */
status = H5Pset_create_intermediate_group(grp_crt_plist, 1);
char *h = (flag[0] == 0) ? "mo" : "ao";
char str[80];
strcati(str, h, "/ints/one_e/hcore");
dataset_id = H5Gcreate2(file_id, str, grp_crt_plist, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(dataset_id);
dims[0] = 1;
int n = o_tot_num[0]*o_tot_num[0];
H5Dcreate_scalar666w(file_id, h, "/ints/one_e/hcore/n", H5T_NATIVE_INT, &n);
dims[0] = o_tot_num[0] * o_tot_num[0];
dims[1] = 2;
H5Dcreate666(file_id, h, "/ints/one_e/hcore/idx", dims, 2, H5T_NATIVE_INT);
H5Dcreate666(file_id, h, "/ints/one_e/hcore/value", dims, 1, H5T_NATIVE_DOUBLE);
strcati(str, h, "/ints/two_e");
dataset_id = H5Gcreate2(file_id, str, grp_crt_plist, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(dataset_id);
H5Dcreate_scalar666w(file_id, h, "/ints/two_e/n", H5T_NATIVE_INT, bi_elec_num);
dims[0] = bi_elec_num[0];
H5Dcreate666(file_id, h, "/ints/two_e/idx", dims, 1, H5T_NATIVE_LLONG);
H5Dcreate666(file_id, h, "/ints/two_e/value", dims, 1, H5T_NATIVE_DOUBLE);
dataset_id = H5Gcreate2(file_id, "nuclei", grp_crt_plist, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(dataset_id);
H5Dcreate_scalar666w(file_id, "nuclei", "/nuclear_repulsion", H5T_NATIVE_DOUBLE, nr);
status = H5Fclose(file_id);
}
void write_hcore_h5_(char *h5path, int *o_tot_num, double *moelec_val, int *flag) {
hid_t file_id; /* identifiers */
herr_t status;
int i, j, k = 0;
long *ptr = (long *)malloc(o_tot_num[0] * o_tot_num[0] * 2 * sizeof(long));
for (i = 0; i < o_tot_num[0]; i++) {
for (j = 0; j < o_tot_num[0]; j++) {
ptr[k] = i;
ptr[k + 1] = j;
k += 2;
}
}
char *h = (flag[0] == 0) ? "mo" : "ao";
file_id = H5Fopen(h5path, H5F_ACC_RDWR, H5P_DEFAULT);
H5Dwrite666(file_id, h, "/ints/one_e/hcore/idx", H5T_NATIVE_LLONG, ptr);
H5Dwrite666(file_id, h, "/ints/one_e/hcore/value", H5T_NATIVE_DOUBLE, moelec_val);
status = H5Fclose(file_id);
}
void write_bielec_h5_(char *h5path, int *bielec_idx, int *bielec_val, int *flag) {
hid_t file_id; /* identifiers */
herr_t status;
file_id = H5Fopen(h5path, H5F_ACC_RDWR, H5P_DEFAULT);
char *h = (flag[0] == 0) ? "mo" : "ao";
H5Dwrite666(file_id, h, "/ints/two_e/idx", H5T_NATIVE_LLONG, bielec_idx);
H5Dwrite666(file_id, h, "/ints/two_e/value", H5T_NATIVE_DOUBLE, bielec_val);
status = H5Fclose(file_id);
}