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stupid but working implementation of read/write_dset decoupled from read_group

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This commit is contained in:
q-posev 2021-03-03 15:59:30 +01:00
parent a9a00e8bec
commit d2efb67a9d
2 changed files with 150 additions and 10 deletions
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78
src/trexio_hdf5.c
View File

@ -411,11 +411,29 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);*/
/* Allocate and read nucleus_coord array */
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
coord[i] = nucleus->coord[i];
}
@ -430,8 +448,7 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);
@ -440,7 +457,60 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
}
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);*/
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
hid_t dset_id, dspace, dtype;
herr_t status;
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
coord_rank, coord_dims, nucleus->coord);
assert (status >= 0);
} else {
dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[2] = {0, 0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == coord_rank);
for (int i=0; i<rrank; i++){
assert (dims[i] == coord_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
trexio_hdf5_free_nucleus(nucleus);

78
src/trexio_hdf5.org
View File

@ -574,11 +574,29 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);*/
/* Allocate and read nucleus_coord array */
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
herr_t status;
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
status = H5LTread_dataset_double(f->nucleus_group,
NUCLEUS_COORD_NAME,
nucleus->coord);
assert (status >= 0);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
coord[i] = nucleus->coord[i];
}
@ -593,8 +611,7 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
/*h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);
@ -603,7 +620,60 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
}
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);*/
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
assert (nucleus != NULL);
trexio_exit_code rc = trexio_hdf5_read_nucleus_num(file, &(nucleus->num));
assert (rc == TREXIO_SUCCESS);
assert (nucleus->num > 0L);
nucleus->coord = (double*) calloc(3 * nucleus->num, sizeof(double));
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
hid_t dset_id, dspace, dtype;
herr_t status;
int coord_rank = 2;
const hsize_t coord_dims[2] = {nucleus->num, 3};
if ( H5LTfind_dataset(f->nucleus_group, NUCLEUS_COORD_NAME) != 1) {
status = H5LTmake_dataset_double (f->nucleus_group, NUCLEUS_COORD_NAME,
coord_rank, coord_dims, nucleus->coord);
assert (status >= 0);
} else {
dset_id = H5Dopen(f->nucleus_group, NUCLEUS_COORD_NAME, H5P_DEFAULT);
assert (dset_id > 0);
dspace = H5Dget_space(dset_id);
assert (dspace > 0);
dtype = H5Dget_type(dset_id);
assert (dtype > 0);
int rrank;
hsize_t dims[2] = {0, 0};
rrank = H5Sget_simple_extent_dims(dspace,
dims, NULL);
assert (rrank == coord_rank);
for (int i=0; i<rrank; i++){
assert (dims[i] == coord_dims[i]);
}
status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, nucleus->coord);
assert (status >= 0);
H5Sclose(dspace);
H5Tclose(dtype);
H5Dclose(dset_id);
}
trexio_hdf5_free_nucleus(nucleus);