diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 82 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 75 |
2 files changed, 78 insertions, 79 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 05a96db..5c858f0 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -433,7 +433,7 @@ static tng_function_status tng_block_hash_generate(tng_gen_block_t block) If the hashes match results is set to TRUE, otherwise it is set to FALSE. */ static tng_function_status hash_match_verify(tng_gen_block_t block, - tng_bool *results) + tng_bool *results) { md5_state_t md5_state; char hash[TNG_HASH_LEN]; @@ -4901,8 +4901,8 @@ static tng_function_status tng_data_block_contents_read static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, tng_gen_block_t block, - int64_t header_start_pos, - int64_t contents_start_pos) + const int64_t header_start_pos, + const int64_t contents_start_pos) { if(block->block_contents) { @@ -5638,10 +5638,10 @@ tng_function_status tng_residue_name_set(tng_trajectory_t tng_data, } tng_function_status tng_residue_atom_add(tng_trajectory_t tng_data, - tng_residue_t residue, - const char *atom_name, - const char *atom_type, - tng_atom_t *atom) + tng_residue_t residue, + const char *atom_name, + const char *atom_type, + tng_atom_t *atom) { int curr_index; tng_atom_t new_atoms, temp_atom, last_atom; @@ -6595,7 +6595,7 @@ tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_medium_stride_length_get(tng_trajectory_t tng_data, +tng_function_status tng_medium_stride_length_get(const tng_trajectory_t tng_data, int64_t *len) { *len = tng_data->medium_stride_length; @@ -6615,7 +6615,7 @@ tng_function_status tng_medium_stride_length_set(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_long_stride_length_get(tng_trajectory_t tng_data, +tng_function_status tng_long_stride_length_get(const tng_trajectory_t tng_data, int64_t *len) { *len = tng_data->long_stride_length; @@ -6635,7 +6635,7 @@ tng_function_status tng_long_stride_length_set(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_input_file_pos_get(tng_trajectory_t tng_data, +tng_function_status tng_input_file_pos_get(const tng_trajectory_t tng_data, int64_t *pos) { *pos = tng_data->input_file_pos; @@ -6643,7 +6643,7 @@ tng_function_status tng_input_file_pos_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_output_file_pos_get(tng_trajectory_t tng_data, +tng_function_status tng_output_file_pos_get(const tng_trajectory_t tng_data, int64_t *pos) { *pos = tng_data->output_file_pos; @@ -6651,7 +6651,7 @@ tng_function_status tng_output_file_pos_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_input_file_len_get(tng_trajectory_t tng_data, +tng_function_status tng_input_file_len_get(const tng_trajectory_t tng_data, int64_t *len) { *len = tng_data->input_file_len; @@ -6659,7 +6659,7 @@ tng_function_status tng_input_file_len_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_num_particles_get(tng_trajectory_t tng_data, +tng_function_status tng_num_particles_get(const tng_trajectory_t tng_data, int64_t *n) { if(tng_data->var_num_atoms_flag == TNG_CONSTANT_N_ATOMS) @@ -6674,7 +6674,7 @@ tng_function_status tng_num_particles_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_num_molecules_get(tng_trajectory_t tng_data, +tng_function_status tng_num_molecules_get(const tng_trajectory_t tng_data, int64_t *n) { int64_t *cnt_list, cnt = 0, i; @@ -6698,7 +6698,7 @@ tng_function_status tng_num_molecules_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_num_frames_per_frame_set_get(tng_trajectory_t tng_data, +tng_function_status tng_num_frames_per_frame_set_get(const tng_trajectory_t tng_data, int64_t *n) { *n = tng_data->frame_set_n_frames; @@ -6708,7 +6708,7 @@ tng_function_status tng_num_frames_per_frame_set_get(tng_trajectory_t tng_data, tng_function_status tng_current_frame_set_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, tng_trajectory_frame_set_t frame_set) { frame_set = &tng_data->current_trajectory_frame_set; @@ -6717,7 +6717,7 @@ tng_function_status tng_current_frame_set_get } tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, - int64_t frame) + const int64_t frame) { int64_t first_frame, last_frame, n_frames_per_frame_set; int64_t long_stride_length, medium_stride_length; @@ -7017,7 +7017,7 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, } tng_function_status tng_frame_set_next_frame_set_file_pos_get - (tng_trajectory_frame_set_t frame_set, + (const tng_trajectory_frame_set_t frame_set, int64_t *pos) { *pos = frame_set->next_frame_set_file_pos; @@ -7026,7 +7026,7 @@ tng_function_status tng_frame_set_next_frame_set_file_pos_get } tng_function_status tng_frame_set_prev_frame_set_file_pos_get - (tng_trajectory_frame_set_t frame_set, + (const tng_trajectory_frame_set_t frame_set, int64_t *pos) { *pos = frame_set->prev_frame_set_file_pos; @@ -7613,7 +7613,7 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, int64_t n_frames, const int64_t n_values_per_frame, const int64_t stride_length, - int64_t codec_id, + const int64_t codec_id, void *new_data) { int i, j, block_index, size, len; @@ -7796,7 +7796,7 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t stride_length, const int64_t num_first_particle, const int64_t n_particles, - int64_t codec_id, + const int64_t codec_id, void *new_data) { int i, j, k, block_index, size, len; @@ -7997,8 +7997,8 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, } tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t start_frame_nr, + const int64_t end_frame_nr, const tng_hash_mode hash_mode) { /* STUB */ @@ -8023,8 +8023,8 @@ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, tng_function_status tng_frame_write_interval (tng_trajectory_t tng_data, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t start_frame_nr, + const int64_t end_frame_nr, const tng_hash_mode hash_mode) { /* STUB */ @@ -8032,9 +8032,9 @@ tng_function_status tng_frame_write_interval } tng_function_status tng_data_values_free(union data_values **values, - int64_t n_frames, - int64_t n_values_per_frame, - tng_data_type type) + const int64_t n_frames, + const int64_t n_values_per_frame, + const tng_data_type type) { int i, j; @@ -8067,10 +8067,10 @@ tng_function_status tng_data_values_free(union data_values **values, } tng_function_status tng_particle_data_values_free(union data_values ***values, - int64_t n_frames, - int64_t n_particles, - int64_t n_values_per_frame, - tng_data_type type) + const int64_t n_frames, + const int64_t n_particles, + const int64_t n_values_per_frame, + const tng_data_type type) { int i, j, k; @@ -8107,7 +8107,7 @@ tng_function_status tng_particle_data_values_free(union data_values ***values, return(TNG_SUCCESS); } tng_function_status tng_data_get(tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, union data_values ***values, int64_t *n_frames, int64_t *n_values_per_frame, @@ -8216,9 +8216,9 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, } tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, - int64_t block_id, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, union data_values ***values, int64_t *n_values_per_frame, tng_data_type *type) @@ -8228,7 +8228,7 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, } tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, union data_values ****values, int64_t *n_frames, int64_t *n_particles, @@ -8382,9 +8382,9 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, } tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, - int64_t block_id, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, union data_values ****values, int64_t *n_particles, int64_t *n_values_per_frame, @@ -8611,7 +8611,7 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_time_get_str(tng_trajectory_t tng_data, +tng_function_status tng_time_get_str(const tng_trajectory_t tng_data, char *time) { struct tm *time_data; diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 9dd47a7..c15bb66 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -315,7 +315,7 @@ tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_medium_stride_length_get(tng_trajectory_t tng_data, +tng_function_status tng_medium_stride_length_get(const tng_trajectory_t tng_data, int64_t *len); /** @@ -335,7 +335,7 @@ tng_function_status tng_medium_stride_length_set(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_long_stride_length_get(tng_trajectory_t tng_data, +tng_function_status tng_long_stride_length_get(const tng_trajectory_t tng_data, int64_t *len); /** @@ -355,7 +355,7 @@ tng_function_status tng_long_stride_length_set(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_input_file_pos_get(tng_trajectory_t tng_data, +tng_function_status tng_input_file_pos_get(const tng_trajectory_t tng_data, int64_t *pos); /** @@ -365,7 +365,7 @@ tng_function_status tng_input_file_pos_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_output_file_pos_get(tng_trajectory_t tng_data, +tng_function_status tng_output_file_pos_get(const tng_trajectory_t tng_data, int64_t *pos); /** @@ -375,7 +375,7 @@ tng_function_status tng_output_file_pos_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_input_file_len_get(tng_trajectory_t tng_data, +tng_function_status tng_input_file_len_get(const tng_trajectory_t tng_data, int64_t *len); /** @@ -387,7 +387,7 @@ tng_function_status tng_input_file_len_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_num_particles_get(tng_trajectory_t tng_data, +tng_function_status tng_num_particles_get(const tng_trajectory_t tng_data, int64_t *n); /** @@ -399,7 +399,7 @@ tng_function_status tng_num_particles_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_num_molecules_get(tng_trajectory_t tng_data, +tng_function_status tng_num_molecules_get(const tng_trajectory_t tng_data, int64_t *n); /** @@ -410,7 +410,7 @@ tng_function_status tng_num_molecules_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_num_frames_per_frame_set_get(tng_trajectory_t tng_data, +tng_function_status tng_num_frames_per_frame_set_get(const tng_trajectory_t tng_data, int64_t *n); /** @@ -421,7 +421,7 @@ tng_function_status tng_num_frames_per_frame_set_get(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_current_frame_set_get - (tng_trajectory_t tng_data, + (const tng_trajectory_t tng_data, tng_trajectory_frame_set_t frame_set); @@ -435,7 +435,7 @@ tng_function_status tng_current_frame_set_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, - int64_t frame); + const int64_t frame); /** * @brief Get the file position of the next frame set in the input file. @@ -446,7 +446,7 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_next_frame_set_file_pos_get - (tng_trajectory_frame_set_t frame_set, + (const tng_trajectory_frame_set_t frame_set, int64_t *pos); /** @@ -458,7 +458,7 @@ tng_function_status tng_frame_set_next_frame_set_file_pos_get * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_prev_frame_set_file_pos_get - (tng_trajectory_frame_set_t frame_set, + (const tng_trajectory_frame_set_t frame_set, int64_t *pos); /** @@ -773,7 +773,7 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, int64_t n_frames, const int64_t n_values_per_frame, const int64_t stride_length, - int64_t codec_id, + const int64_t codec_id, void *new_data); @@ -811,7 +811,7 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t stride_length, const int64_t first_particle_number, const int64_t n_particles, - int64_t codec_id, + const int64_t codec_id, void *new_data); @@ -832,8 +832,8 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t start_frame_nr, + const int64_t end_frame_nr, const tng_hash_mode hash_mode); /** @@ -852,8 +852,8 @@ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t start_frame_nr, + const int64_t end_frame_nr, const tng_hash_mode hash_mode); /** @@ -866,9 +866,9 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_data_values_free(union data_values **values, - int64_t n_frames, - int64_t n_values_per_frame, - tng_data_type type); + const int64_t n_frames, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Free data is an array of values (3D). @@ -881,10 +881,10 @@ tng_function_status tng_data_values_free(union data_values **values, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_particle_data_values_free(union data_values ***values, - int64_t n_frames, - int64_t n_particles, - int64_t n_values_per_frame, - tng_data_type type); + const int64_t n_frames, + const int64_t n_particles, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Retrieve non-particle data, from the last read frame set. @@ -906,7 +906,7 @@ tng_function_status tng_particle_data_values_free(union data_values ***values, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_data_get(tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, union data_values ***values, int64_t *n_frames, int64_t *n_values_per_frame, @@ -933,9 +933,9 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, - int64_t block_id, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, union data_values ***values, int64_t *n_values_per_frame, tng_data_type *type); @@ -965,7 +965,7 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, - int64_t block_id, + const int64_t block_id, union data_values ****values, int64_t *n_frames, int64_t *n_particles, @@ -984,15 +984,13 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, * @param block_id is the id number of the particle data block to read. * @param start_frame_nr is the index number of the first frame to read. * @param end_frame_nr is the index number of the last frame to read. - * @param first_particle_number is the number of the first particle, for which to - * retrieve data. - * @param last_particle_number is the number of the last particle, for which to - * retrieve data. * @param values is a pointer to a 3-dimensional array (memory unallocated), which * will be filled with data. The array will be sized * (n_frames * n_particles * n_values_per_frame). * Since ****values is allocated in this function it is the callers * responsibility to free the memory. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. * @param n_values_per_frame is set to the number of values per frame in the data. * This is needed to properly reach and/or free the data afterwards. * @param type is set to the data type of the data in the array. @@ -1000,9 +998,9 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, - int64_t block_id, - int64_t start_frame_nr, - int64_t end_frame_nr, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, union data_values ****values, int64_t *n_particles, int64_t *n_values_per_frame, @@ -1015,7 +1013,8 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_time_get_str(tng_trajectory_t tng_data, char *time); +tng_function_status tng_time_get_str(const tng_trajectory_t tng_data, + char *time); #ifdef __cplusplus } /* end extern "C" */ |