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Merge pull request #15 from TREX-CoE/append_mode

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Append mode for trexio_open; fixes #13
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Evgeny Posenitskiy 2021-03-03 13:21:18 +01:00 committed by GitHub
commit 563d395d24
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3 changed files with 79 additions and 17 deletions
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30
src/test.c
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@ -59,6 +59,18 @@ int test_h5write() {
rc = trexio_write_nucleus_num(file,25);
assert (rc != TREXIO_SUCCESS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
file = trexio_open(file_name, 'a', TREXIO_HDF5);
assert (file != NULL);
// works: try to read the nucleus_num from existing file
rc = trexio_read_nucleus_num(file,&num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// works: try to rewrite the nucleus_coord
coord[0] = 666.666;
rc = trexio_write_nucleus_coord(file,coord);
@ -79,6 +91,7 @@ int test_h5read() {
int64_t num;
double* coord;
// test reading existing file [created by test_h5write()], should work
file = trexio_open(file_name, 'r', TREXIO_HDF5);
assert (file != NULL);
@ -100,6 +113,23 @@ int test_h5read() {
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// test reading non-existing file, should fail and return NULL
const char* file_name2 = "test_nonexisting.h5";
trexio_t* file2 = NULL;
file2 = trexio_open(file_name2, 'r', TREXIO_HDF5);
assert (file2 == NULL);
// test appending non-existing file, should create it
const char* file_name3 = "test_append.h5";
trexio_t* file3 = NULL;
file3 = trexio_open(file_name3, 'a', TREXIO_HDF5);
assert (file3 != NULL);
rc = trexio_close(file3);
assert (rc == TREXIO_SUCCESS);
free(coord);
return 0;

2
src/trexio.org
View File

@ -164,7 +164,7 @@ 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 >= 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;

64
src/trexio_hdf5.org
View File

@ -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: