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-rw-r--r--include/tng_io.h56
-rw-r--r--src/lib/tng_io.c119
2 files changed, 96 insertions, 79 deletions
diff --git a/include/tng_io.h b/include/tng_io.h
index 1118b15..45cb1d8 100644
--- a/include/tng_io.h
+++ b/include/tng_io.h
@@ -669,7 +669,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set
* could not be retrieved.
*/
tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_get
- (tng_trajectory_t tng_data, tng_file_endianness *endianness);
+ (const tng_trajectory_t tng_data, tng_file_endianness *endianness);
/**
* @brief Set the endianness of the output file.
@@ -1294,7 +1294,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
* @return TNG_SUCCESS (0) if successful.
*/
tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
tng_trajectory_frame_set_t *frame_set_p);
/**
@@ -1527,8 +1527,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set
* has occurred or TNG_CRITICAL (2) if a major error has occured.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
int64_t *cnt);
/**
@@ -1612,8 +1612,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_system_copy(tng_trajectory_t
* @return TNG_SUCCESS (0) if successful.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_num_chains_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
int64_t *n);
/**
@@ -1644,8 +1644,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_of_index_get
* @return TNG_SUCCESS (0) if successful.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_num_residues_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
int64_t *n);
/**
@@ -1661,9 +1661,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_residues_get
* residue is not found.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_residue_of_index_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
+ const int64_t index,
tng_residue_t *residue);
/**
@@ -1676,8 +1676,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_residue_of_index_get
* @return TNG_SUCCESS (0) if successful.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_num_atoms_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
int64_t *n);
/**
@@ -1693,9 +1693,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_atoms_get
* atom is not found.
*/
tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
+ const int64_t index,
tng_atom_t *atom);
/**
@@ -1867,9 +1867,9 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_num_residues_get
* residue is not found.
*/
tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get
- (tng_trajectory_t tng_data,
- tng_chain_t chain,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_chain_t chain,
+ const int64_t index,
tng_residue_t *residue);
/**
@@ -1999,9 +1999,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_num_atoms_get
* atom is not found.
*/
tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get
- (tng_trajectory_t tng_data,
- tng_residue_t residue,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_residue_t residue,
+ const int64_t index,
tng_atom_t *atom);
/**
@@ -2060,7 +2060,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add
* @pre \code atom != 0 \endcode The atom must not be NULL.
* @return TNG_SUCCESS (0) if successful.
*/
-tng_function_status tng_atom_residue_get(tng_trajectory_t tng_data,
+tng_function_status tng_atom_residue_get(const tng_trajectory_t tng_data,
const tng_atom_t atom,
tng_residue_t *residue);
@@ -2611,7 +2611,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set
* frame set or TNG_CRITICAL(2) if a major error has occured.
*/
tng_function_status DECLSPECDLLEXPORT tng_first_frame_nr_of_next_frame_set_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t *frame);
/**
@@ -2736,7 +2736,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get
* TNG_CRITICAL (2) if a major error has occured.
*/
tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t block_id,
int *block_dependency);
@@ -2753,7 +2753,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get
* TNG_CRITICAL (2) if a major error has occured.
*/
tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t block_id,
int64_t *n_values_per_frame);
@@ -3229,7 +3229,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get
* has occurred or TNG_CRITICAL (2) if a major error has occured.
*/
tng_function_status DECLSPECDLLEXPORT tng_data_get_stride_length
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
const int64_t block_id,
int64_t frame,
int64_t *stride_length);
@@ -4681,7 +4681,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write
tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get
(tng_trajectory_t tng_data,
const int64_t block_id,
- char *codec_id,
+ int64_t *codec_id,
float *factor);
/** @brief High-level function for determining the next frame with data and what
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index e201da2..33ca978 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -683,7 +683,7 @@ static tng_function_status tng_input_file_init(tng_trajectory_t tng_data)
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
- tng_data->input_file = fopen(tng_data->input_file_path, "r");
+ tng_data->input_file = fopen(tng_data->input_file_path, "rb");
if(!tng_data->input_file)
{
fprintf(stderr, "TNG library: Cannot open file %s. %s: %d\n",
@@ -710,7 +710,7 @@ static tng_function_status tng_output_file_init(tng_trajectory_t tng_data)
return(TNG_CRITICAL);
}
- tng_data->output_file = fopen(tng_data->output_file_path, "w+");
+ tng_data->output_file = fopen(tng_data->output_file_path, "wb+");
if(!tng_data->output_file)
{
@@ -733,7 +733,6 @@ static tng_function_status tng_block_init(struct tng_gen_block **block_p)
tng_gen_block_t block;
*block_p = malloc(sizeof(struct tng_gen_block));
-
if(!*block_p)
{
fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
@@ -3865,7 +3864,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
return(TNG_FAILURE);
}
- f_precision = 1/tng_data->compression_precision;
+ f_precision = 1/(float)tng_data->compression_precision;
d_precision = 1/tng_data->compression_precision;
if(block->id == TNG_TRAJ_POSITIONS)
@@ -4216,6 +4215,12 @@ static tng_function_status tng_gzip_compress(tng_trajectory_t tng_data,
max_len = compressBound(len);
dest = malloc(max_len);
+ if(!dest)
+ {
+ fprintf(stderr, "TNG library: Cannot allocate memory (%ld bytes). %s: %d\n",
+ max_len, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
stat = compress(dest, &max_len, start_pos, len);
if(stat != (unsigned long)Z_OK)
@@ -4271,6 +4276,12 @@ static tng_function_status tng_gzip_uncompress(tng_trajectory_t tng_data,
offset = (char *)start_pos - (char *)block->block_contents;
dest = malloc(uncompressed_len);
+ if(!dest)
+ {
+ fprintf(stderr, "TNG library: Cannot allocate memory (%lud bytes). %s: %d\n",
+ uncompressed_len, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
stat = uncompress(dest, &uncompressed_len, (Bytef *) start_pos,
block->block_contents_size - offset);
@@ -6242,7 +6253,6 @@ static tng_function_status tng_data_block_meta_information_read
{
meta_size = 3 * sizeof(char) + sizeof(double) + 6 * sizeof(int64_t);
contents = malloc(meta_size);
-
if(!contents)
{
fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
@@ -6528,6 +6538,13 @@ static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data,
}
block->block_contents = malloc(block->block_contents_size);
+ if(!block->block_contents)
+ {
+ fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
+ block->block_contents_size, __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+
fseek(tng_data->output_file, (long)contents_start_pos, SEEK_SET);
if(fread(block->block_contents, block->block_contents_size, 1,
tng_data->output_file) == 0)
@@ -7047,7 +7064,7 @@ static tng_function_status tng_frame_set_finalize
// }
*/
-tng_function_status tng_atom_residue_get(tng_trajectory_t tng_data,
+tng_function_status tng_atom_residue_get(const tng_trajectory_t tng_data,
const tng_atom_t atom,
tng_residue_t *residue)
{
@@ -7060,7 +7077,7 @@ tng_function_status tng_atom_residue_get(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
-tng_function_status tng_atom_name_get(tng_trajectory_t tng_data,
+tng_function_status tng_atom_name_get(const tng_trajectory_t tng_data,
const tng_atom_t atom,
char *name,
const int max_len)
@@ -7114,7 +7131,7 @@ tng_function_status tng_atom_name_set(tng_trajectory_t tng_data,
return(TNG_SUCCESS);
}
-tng_function_status tng_atom_type_get(tng_trajectory_t tng_data,
+tng_function_status tng_atom_type_get(const tng_trajectory_t tng_data,
const tng_atom_t atom,
char *type,
const int max_len)
@@ -7384,7 +7401,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add
return(TNG_SUCCESS);
}
-tng_function_status tng_molecule_name_get(tng_trajectory_t tng_data,
+tng_function_status tng_molecule_name_get(const tng_trajectory_t tng_data,
const tng_molecule_t molecule,
char *name,
const int max_len)
@@ -7440,8 +7457,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set
}
tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
int64_t *cnt)
{
int64_t i, index = -1;
@@ -7735,9 +7752,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_residues_get
}
tng_function_status DECLSPECDLLEXPORT tng_molecule_residue_of_index_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
+ const int64_t index,
tng_residue_t *residue)
{
(void) tng_data;
@@ -7768,9 +7785,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_num_atoms_get
}
tng_function_status DECLSPECDLLEXPORT tng_molecule_atom_of_index_get
- (tng_trajectory_t tng_data,
- tng_molecule_t molecule,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_molecule_t molecule,
+ const int64_t index,
tng_atom_t *atom)
{
(void) tng_data;
@@ -8035,9 +8052,9 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_num_residues_get
}
tng_function_status DECLSPECDLLEXPORT tng_chain_residue_of_index_get
- (tng_trajectory_t tng_data,
- tng_chain_t chain,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_chain_t chain,
+ const int64_t index,
tng_residue_t *residue)
{
(void) tng_data;
@@ -8192,7 +8209,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add
return(stat);
}
-tng_function_status tng_residue_name_get(tng_trajectory_t tng_data,
+tng_function_status tng_residue_name_get(const tng_trajectory_t tng_data,
const tng_residue_t residue,
char *name,
const int max_len)
@@ -8261,9 +8278,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_num_atoms_get
}
tng_function_status DECLSPECDLLEXPORT tng_residue_atom_of_index_get
- (tng_trajectory_t tng_data,
- tng_residue_t residue,
- int64_t index,
+ (const tng_trajectory_t tng_data,
+ const tng_residue_t residue,
+ const int64_t index,
tng_atom_t *atom)
{
tng_chain_t chain;
@@ -9818,7 +9835,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set
strncpy(tng_data->output_file_path, file_name, len);
- tng_data->output_file = fopen(tng_data->output_file_path, "r+");
+ tng_data->output_file = fopen(tng_data->output_file_path, "rb+");
if(!tng_data->output_file)
{
fprintf(stderr, "TNG library: Cannot open file %s. %s: %d\n",
@@ -9830,7 +9847,7 @@ tng_function_status DECLSPECDLLEXPORT tng_output_append_file_set
}
tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_get
- (tng_trajectory_t tng_data, tng_file_endianness *endianness)
+ (const tng_trajectory_t tng_data, tng_file_endianness *endianness)
{
tng_endianness_32 end_32;
tng_endianness_64 end_64;
@@ -10838,7 +10855,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
int64_t *n)
{
int64_t long_stride_length, medium_stride_length;
- int64_t file_pos, orig_frame_set_file_pos;
+ long file_pos, orig_frame_set_file_pos;
tng_trajectory_frame_set_t frame_set;
struct tng_trajectory_frame_set orig_frame_set;
tng_gen_block_t block;
@@ -10853,18 +10870,18 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
frame_set = &tng_data->current_trajectory_frame_set;
orig_frame_set_file_pos = tng_data->current_trajectory_frame_set_input_file_pos;
- file_pos = tng_data->first_trajectory_frame_set_input_file_pos;
+ file_pos = (long)tng_data->first_trajectory_frame_set_input_file_pos;
tng_block_init(&block);
fseek(tng_data->input_file,
- (long)file_pos,
+ file_pos,
SEEK_SET);
- tng_data->current_trajectory_frame_set_input_file_pos = (long)file_pos;
+ tng_data->current_trajectory_frame_set_input_file_pos = file_pos;
/* Read block headers first to see what block is found. */
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %ld. %s: %d\n", file_pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
@@ -10884,18 +10901,18 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
/* Take long steps forward until a long step forward would be too long or
* the last frame set is found */
- file_pos = frame_set->long_stride_next_frame_set_file_pos;
+ file_pos = (long)frame_set->long_stride_next_frame_set_file_pos;
while(file_pos > 0)
{
if(file_pos > 0)
{
cnt += long_stride_length;
- fseek(tng_data->input_file, (long)file_pos, SEEK_SET);
+ fseek(tng_data->input_file, file_pos, SEEK_SET);
/* Read block headers first to see what block is found. */
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %ld. %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
@@ -10908,25 +10925,25 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
return(TNG_CRITICAL);
}
}
- file_pos = frame_set->long_stride_next_frame_set_file_pos;
+ file_pos = (long)frame_set->long_stride_next_frame_set_file_pos;
}
/* Take medium steps forward until a medium step forward would be too long
* or the last frame set is found */
- file_pos = frame_set->medium_stride_next_frame_set_file_pos;
+ file_pos = (long)frame_set->medium_stride_next_frame_set_file_pos;
while(file_pos > 0)
{
if(file_pos > 0)
{
cnt += medium_stride_length;
fseek(tng_data->input_file,
- (long)file_pos,
+ file_pos,
SEEK_SET);
/* Read block headers first to see what block is found. */
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %ld. %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
@@ -10939,24 +10956,24 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
return(TNG_CRITICAL);
}
}
- file_pos = frame_set->medium_stride_next_frame_set_file_pos;
+ file_pos = (long)frame_set->medium_stride_next_frame_set_file_pos;
}
/* Take one step forward until the last frame set is found */
- file_pos = frame_set->next_frame_set_file_pos;
+ file_pos = (long)frame_set->next_frame_set_file_pos;
while(file_pos > 0)
{
if(file_pos > 0)
{
++cnt;
fseek(tng_data->input_file,
- (long)file_pos,
+ file_pos,
SEEK_SET);
/* Read block headers first to see what block is found. */
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %ld. %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
@@ -10969,7 +10986,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
return(TNG_CRITICAL);
}
}
- file_pos = frame_set->next_frame_set_file_pos;
+ file_pos = (long)frame_set->next_frame_set_file_pos;
}
tng_block_destroy(&block);
@@ -10988,7 +11005,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get
}
tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
tng_trajectory_frame_set_t *frame_set_p)
{
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
@@ -12621,7 +12638,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set
}
tng_function_status DECLSPECDLLEXPORT tng_first_frame_nr_of_next_frame_set_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t *frame)
{
long file_pos, next_frame_set_file_pos;
@@ -13096,7 +13113,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_name_get
}
tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t block_id,
int *block_dependency)
{
@@ -13170,7 +13187,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_dependency_get
}
tng_function_status DECLSPECDLLEXPORT tng_data_block_num_values_per_frame_get
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
int64_t block_id,
int64_t *n_values_per_frame)
{
@@ -15958,7 +15975,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get
}
tng_function_status DECLSPECDLLEXPORT tng_data_get_stride_length
- (tng_trajectory_t tng_data,
+ (const tng_trajectory_t tng_data,
const int64_t block_id,
int64_t frame,
int64_t *stride_length)
@@ -18104,7 +18121,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write
tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get
(tng_trajectory_t tng_data,
const int64_t block_id,
- char *codec_id,
+ int64_t *codec_id,
float *factor)
{
tng_trajectory_frame_set_t frame_set;
@@ -18202,12 +18219,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_frame_current_compression_get
if(block_type == TNG_PARTICLE_BLOCK_DATA)
{
*codec_id = p_data->codec_id;
- *factor = p_data->compression_multiplier;
+ *factor = (float)p_data->compression_multiplier;
}
else if(block_type == TNG_NON_PARTICLE_BLOCK_DATA)
{
*codec_id = np_data->codec_id;
- *factor = np_data->compression_multiplier;
+ *factor = (float)np_data->compression_multiplier;
}
return(TNG_SUCCESS);
}
contact: Jan Huwald // Impressum