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working append mode for hdf5

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q-posev 2021-03-03 11:49:21 +01:00
parent d3f2fd6263
commit 886a3d2162
1 changed files with 48 additions and 16 deletions
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64
src/trexio_hdf5.org
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@ -159,26 +159,59 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
/* If file doesn't exist, create it */
int f_ishere = 0;
int f_exists = 0;
struct stat st;
if (stat(file->file_name, &st) == 0) {
printf("%s \n","HDF5 file already exists");
// RDWR OR RDONLY ???
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
f_ishere = 1;
if (stat(file->file_name, &st) == 0) f_exists = 1;
if (f_exists == 1) {
switch (file->mode) {
case 'r':
// reading the existing file -> open as RDONLY
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
break;
case 'a':
// appending the existing file -> open as RDWR
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
break;
case 'w':
// writing the existing file -> overwrite it (_TRUNC) [_EXCL | H5F_ACC_DEBUG as an alternative]
f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
break;
}
} else {
f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
f_ishere = 0;
switch (file->mode) {
case 'r':
// reading non-existing file -> error
return TREXIO_FAILURE;
case 'a':
case 'w':
// appending or writing non-existing file -> create it
f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
break;
}
}
/* Create groups in the hdf5 file */
if (f_ishere == 0){
f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} else {
f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);
/* Create or open groups in the hdf5 file assuming that they exist if file exists */
switch (file->mode) {
case 'r':
case 'a':
if (f_exists == 1) {
f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);
} else {
f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
break;
case 'w':
f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
break;
}
assert (f->nucleus_group > 0L);
//assert (f->electron_group > 0L);
@ -578,7 +611,6 @@ trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const dou
}
#+end_src
** TODO Read/Write the charge attribute
* File suffixes :noxport: