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make consistent with _hdf5.org file

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q-posev 2021-03-03 13:33:15 +01:00
parent 563d395d24
commit a9a00e8bec
3 changed files with 55 additions and 21 deletions
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3
src/Makefile
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@ -46,7 +46,8 @@ test: libtrexio.so test.c
$(CC) $(CFLAGS) $(INCLUDE) -Wl,-rpath,$(PWD) -L. test.c -ltrexio $(LIBS) -o test $(CC) $(CFLAGS) $(INCLUDE) -Wl,-rpath,$(PWD) -L. test.c -ltrexio $(LIBS) -o test
clean: clean:
rm -f *.o libtrexio.so test test_write.h5 rm -f *.o libtrexio.so test test_*.h5
rm -r trexio_test/
%.o: %.c $(HEADER_FILES) %.o: %.c $(HEADER_FILES)
$(CC) $(CFLAGS) $(INCLUDE) -c $*.c -o $*.o $(CC) $(CFLAGS) $(INCLUDE) -c $*.c -o $*.o

2
src/trexio.c
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@ -27,7 +27,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
if (back_end < 0) return NULL; if (back_end < 0) return NULL;
if (back_end >= TREXIO_INVALID_BACK_END) return NULL; if (back_end >= TREXIO_INVALID_BACK_END) return NULL;
if (mode != 'r' && mode != 'w') return NULL; if (mode != 'r' && mode != 'w' && mode != 'a') return NULL;
trexio_t* result = NULL; trexio_t* result = NULL;

63
src/trexio_hdf5.c
View File

@ -7,10 +7,10 @@
#include "trexio_hdf5.h" #include "trexio_hdf5.h"
#define NUCLEUS_GROUP_NAME "nucleus" #define NUCLEUS_GROUP_NAME "nucleus"
#define NUCLEUS_NUM_NAME "nucleus_num" #define NUCLEUS_NUM_NAME "nucleus_num"
#define NUCLEUS_CHARGE_NAME "nucleus_charge" #define NUCLEUS_CHARGE_NAME "nucleus_charge"
#define NUCLEUS_COORD_NAME "nucleus_coord" #define NUCLEUS_COORD_NAME "nucleus_coord"
/* /*
* Currently H5LTread_dataset_ is used instead of this function * Currently H5LTread_dataset_ is used instead of this function
@ -68,26 +68,59 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
trexio_hdf5_t* f = (trexio_hdf5_t*) file; trexio_hdf5_t* f = (trexio_hdf5_t*) file;
/* If file doesn't exist, create it */ /* If file doesn't exist, create it */
int f_ishere = 0; int f_exists = 0;
struct stat st; struct stat st;
if (stat(file->file_name, &st) == 0) { if (stat(file->file_name, &st) == 0) f_exists = 1;
printf("%s \n","HDF5 file already exists");
// RDWR OR RDONLY ??? 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); f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
f_ishere = 1; break;
} else { 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); f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
f_ishere = 0; 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 { } else {
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 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->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
//f->electron_group = H5Gopen(f->file_id, ELECTRON_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->nucleus_group > 0L);
//assert (f->electron_group > 0L); //assert (f->electron_group > 0L);