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-rw-r--r--src/lib/tng_io.c89
1 files changed, 86 insertions, 3 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index f016ca9..07e8a28 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -835,6 +835,8 @@ static tng_function_status tng_block_header_read
{
int len, offset = 0;
+ TNG_ASSERT(block != 0, "TNG library: Trying to read to uninitialized block (NULL pointer).");
+
if(tng_input_file_init(tng_data) != TNG_SUCCESS)
{
return(TNG_CRITICAL);
@@ -853,7 +855,7 @@ static tng_function_status tng_block_header_read
if(ftell(tng_data->input_file) < 9)
{
/* File is little endian */
- if ( *(const char*)&block->header_contents_size != 0x00 &&
+ if ( *((const char*)&block->header_contents_size) != 0x00 &&
*((const char*)(&block->header_contents_size) + 7) == 0x00)
{
/* If the architecture endianness is little endian no byte swap
@@ -8430,6 +8432,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
for(i = 0; i < tng_data->n_molecules; i++)
{
@@ -8471,6 +8478,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8510,6 +8522,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
*n_bonds = 0;
/* First count the total number of bonds to allocate memory */
for(i = 0; i < tng_data->n_molecules; i++)
@@ -8518,6 +8535,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get
mol_cnt = molecule_cnt_list[i];
*n_bonds += mol_cnt * mol->n_bonds;
}
+ if(*n_bonds == 0)
+ {
+ return(TNG_SUCCESS);
+ }
+
*from_atoms = malloc(sizeof(int64_t) * (*n_bonds));
if(!*from_atoms)
{
@@ -8573,6 +8595,11 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8620,6 +8647,11 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8666,6 +8698,11 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8707,6 +8744,11 @@ tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8752,6 +8794,11 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -8795,6 +8842,11 @@ tng_function_status tng_atom_type_of_particle_nr_get
tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list);
+ if(!molecule_cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = 0; i < tng_data->n_molecules; i++)
{
mol = &tng_data->molecules[i];
@@ -10610,6 +10662,11 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get
tng_molecule_cnt_list_get(tng_data, &cnt_list);
+ if(!cnt_list)
+ {
+ return(TNG_FAILURE);
+ }
+
for(i = tng_data->n_molecules; i --;)
{
cnt += cnt_list[i];
@@ -14767,6 +14824,13 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get
(long)tng_data->current_trajectory_frame_set_input_file_pos,
SEEK_SET);
stat = tng_block_header_read(tng_data, block);
+ if(stat != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot read block header. %s: %d\n",
+ __FILE__, __LINE__);
+ return(stat);
+ }
+
fseek(tng_data->input_file, (long)block->block_contents_size, SEEK_CUR);
}
file_pos = ftell(tng_data->input_file);
@@ -15604,6 +15668,13 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get
(long)tng_data->current_trajectory_frame_set_input_file_pos,
SEEK_SET);
stat = tng_block_header_read(tng_data, block);
+ if(stat != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot read block header. %s: %d\n",
+ __FILE__, __LINE__);
+ return(stat);
+ }
+
fseek(tng_data->input_file, (long)block->block_contents_size, SEEK_CUR);
}
file_pos = ftell(tng_data->input_file);
@@ -16382,7 +16453,13 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read
}
if(frame_set->prev_frame_set_file_pos != frame_set_file_pos)
{
- tng_num_frames_get(tng_data, &n_frames);
+ stat = tng_num_frames_get(tng_data, &n_frames);
+ if(stat != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot get number of frames. %s: %d\n",
+ __FILE__, __LINE__);
+ return(stat);
+ }
if(i < n_frames)
{
fprintf(stderr, "TNG library: Cannot find frame set of frame %"PRId64". %s: %d\n",
@@ -16551,6 +16628,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read
if(frame_set->prev_frame_set_file_pos != frame_set_file_pos)
{
tng_num_frames_get(tng_data, &n_frames);
+ if(stat != TNG_SUCCESS)
+ {
+ fprintf(stderr, "TNG library: Cannot get number of frames. %s: %d\n",
+ __FILE__, __LINE__);
+ return(stat);
+ }
if(i < n_frames)
{
fprintf(stderr, "TNG library: Cannot find frame set of frame %"PRId64". %s: %d\n",
@@ -16893,7 +16976,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set
tng_trajectory_frame_set_t frame_set;
tng_particle_data_t p_data;
tng_non_particle_data_t np_data;
- int64_t n_particles, n_frames = 100*i;
+ int64_t n_particles, n_frames;
tng_function_status stat;
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
contact: Jan Huwald // Impressum