diff options
| -rw-r--r-- | include/tng_io.h | 13 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 169 |
2 files changed, 133 insertions, 49 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 4df522b..7028bdc 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1418,6 +1418,19 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add tng_molecule_t *molecule); /** + * @brief Add an existing molecule (from a molecule container) to the trajectory. + * @param tng_data is the trajectory data container containing the block.. + * @param molecule is the molecule to add to the trajectory. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major error + * has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add + (tng_trajectory_t tng_data, + tng_molecule_t molecule); + +/** * @brief Set the name of a molecule. * @param tng_data is the trajectory data container containing the molecule.. * @param molecule is the molecule to rename. diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index b4dcb73..5349f20 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -4016,9 +4016,9 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, } offset = (unsigned long)((char *)start_pos - block->block_contents); - + block->block_contents_size = new_len + offset; - + temp = realloc(block->block_contents, block->block_contents_size); if(!temp) { @@ -4055,7 +4055,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, unsigned long offset; int result; (void)tng_data; - + TNG_ASSERT(uncompressed_len, "TNG library: The full length of the uncompressed data must be > 0."); if(block->id != TNG_TRAJ_POSITIONS && @@ -4070,7 +4070,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, printf("TNG library: Data type not supported.\n"); return(TNG_FAILURE); } - + if(type == TNG_FLOAT_DATA) { f_dest = malloc(uncompressed_len); @@ -4311,7 +4311,7 @@ static tng_function_status tng_allocate_particle_data_mem data->stride_length = tng_max_i64(1, stride_length); data->n_values_per_frame = n_values_per_frame; frame_alloc = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length; - + if(data->datatype == TNG_CHAR_DATA) { data->strings = malloc(sizeof(char ***) * frame_alloc); @@ -4560,7 +4560,7 @@ static tng_function_status tng_particle_data_read default: size = sizeof(double); } - + /* If the block does not exist, create it */ if(tng_particle_data_find(tng_data, block->id, &data) != TNG_SUCCESS) { @@ -4624,7 +4624,7 @@ static tng_function_status tng_particle_data_read } n_frames_div = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length; - + if(codec_id != TNG_UNCOMPRESSED) { data_size = (unsigned long)(n_frames_div * size * n_particles * n_values); @@ -6969,8 +6969,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add const char *name, tng_molecule_t *molecule) { - int id; - int64_t i; + int64_t id, i; tng_bool found_id = TNG_TRUE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); @@ -7068,6 +7067,78 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add return(stat); } +tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add + (tng_trajectory_t tng_data, + tng_molecule_t molecule) +{ + tng_bool found_id = TNG_TRUE; + tng_molecule_t new_molecules; + int64_t *new_molecule_cnt_list, i, id; + + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + + /* Find an unused ID */ + id = 0; + while(found_id) + { + found_id = TNG_FALSE; + for(i = tng_data->n_molecules; i--;) + { + if(tng_data->molecules[i].id == id) + { + found_id = TNG_TRUE; + i = 0; + } + } + if(found_id) + { + id++; + } + } + + new_molecules = realloc(tng_data->molecules, + sizeof(struct tng_molecule) * + (tng_data->n_molecules + 1)); + + if(!new_molecules) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(struct tng_molecule) * (tng_data->n_molecules + 1), + __FILE__, __LINE__); + free(tng_data->molecules); + tng_data->molecules = 0; + return(TNG_CRITICAL); + } + + new_molecule_cnt_list = realloc(tng_data->molecule_cnt_list, + sizeof(int64_t) * + (tng_data->n_molecules + 1)); + + if(!new_molecule_cnt_list) + { + printf("TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * (tng_data->n_molecules + 1), + __FILE__, __LINE__); + free(tng_data->molecule_cnt_list); + tng_data->molecule_cnt_list = 0; + free(new_molecules); + return(TNG_CRITICAL); + } + + tng_data->molecules = new_molecules; + tng_data->molecule_cnt_list = new_molecule_cnt_list; + + new_molecules[tng_data->n_molecules] = *molecule; + + tng_data->molecule_cnt_list[tng_data->n_molecules] = 0; + + molecule->id = id; + + tng_data->n_molecules++; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set (tng_trajectory_t tng_data, tng_molecule_t molecule, @@ -9771,7 +9842,7 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set TNG_ASSERT(n >= 0, "TNG library: The number of molecules must be >= 0"); diff = n - tng_data->n_particles; - + if(diff == 0) { return(stat); @@ -11087,7 +11158,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_ tng_data->input_file_len = ftell(tng_data->input_file); 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) @@ -11115,7 +11186,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_ } } file_pos = ftell(tng_data->input_file); - + found_flag = 0; /* Read only blocks of the requested ID @@ -11163,7 +11234,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_ } tng_block_destroy(&block); - + if(found_flag) { return(TNG_SUCCESS); @@ -13334,7 +13405,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get } } } - + data->last_retrieved_frame = frame_set->first_frame + data->n_frames - 1; return(TNG_SUCCESS); @@ -13451,7 +13522,7 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, *values = temp; memcpy(*values, data->values, data_size); - + data->last_retrieved_frame = frame_set->first_frame + data->n_frames - 1; return(TNG_SUCCESS); @@ -13655,7 +13726,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } data->last_retrieved_frame = end_frame_nr; - + return(TNG_SUCCESS); } @@ -13888,7 +13959,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get } np_data->last_retrieved_frame = end_frame_nr; - + return(TNG_SUCCESS); } @@ -14090,7 +14161,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get } data->last_retrieved_frame = frame_set->first_frame + data->n_frames - 1; - + return(TNG_SUCCESS); } @@ -14251,7 +14322,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get } data->last_retrieved_frame = frame_set->first_frame + data->n_frames - 1; - + return(TNG_SUCCESS); } @@ -14491,7 +14562,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } data->last_retrieved_frame = end_frame_nr; - + return(TNG_SUCCESS); } @@ -14724,7 +14795,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get } p_data->last_retrieved_frame = end_frame_nr; - + return(TNG_SUCCESS); } @@ -14739,12 +14810,12 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get_stride_length tng_particle_data_t p_data; long file_pos; int is_particle_data; - + if(tng_data->current_trajectory_frame_set_input_file_pos <= 0) { frame = 0; } - + if(frame >= 0) { stat = tng_frame_set_of_frame_find(tng_data, frame); @@ -15212,15 +15283,15 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read int64_t i, data_size, n_particles; void *temp; long file_pos; - + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(values, "TNG library: The pointer to the values array must not be a NULL pointer"); TNG_ASSERT(data_type, "TNG library: The pointer to the data type of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_frame_number, "TNG library: The pointer to the frame number of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_time, "TNG library: The pointer to the time of the returned data must not be a NULL pointer"); - + frame_set = &tng_data->current_trajectory_frame_set; - + stat = tng_particle_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { @@ -15268,7 +15339,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read *retrieved_frame_number = i; if(frame_set->first_frame_time >= 0 && tng_data->time_per_frame >= 0) { - *retrieved_time = frame_set->first_frame_time + + *retrieved_time = frame_set->first_frame_time + (i - frame_set->first_frame) * tng_data->time_per_frame; } @@ -15276,11 +15347,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read { *retrieved_time = 0; } - + // printf("TEMP: First frame time: %e, i: %"PRId64", First frame: %"PRId64", Time per frame: %e\n", // frame_set->first_frame_time, i, frame_set->first_frame, tng_data->time_per_frame); // printf("TNG library: TEMP: first_frame_with_data: %"PRId64"\n", data->first_frame_with_data); - + if(data->stride_length > 1) { i = (i - data->first_frame_with_data) / data->stride_length; @@ -15289,11 +15360,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read { i = (i - frame_set->first_frame) / data->stride_length; } - + tng_num_particles_get(tng_data, &n_particles); - + *data_type = data->datatype; - + switch(*data_type) { case TNG_CHAR_DATA: @@ -15308,9 +15379,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read default: size = sizeof(double); } - + data_size = size * n_particles * data->n_values_per_frame; - + // printf("TNG library: TEMP: i = %"PRId64", data_size = %"PRId64", size = %d, n_particles = %"PRId64", n_values_per_frame = %"PRId64"\n", // i, data_size, size, n_particles, data->n_values_per_frame); @@ -15323,11 +15394,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read *values = 0; return(TNG_CRITICAL); } - + *values = temp; - + memcpy(*values, (char *)data->values + i * data_size, data_size); - + return(TNG_SUCCESS); } @@ -15346,15 +15417,15 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read int64_t i, data_size; void *temp; long file_pos; - + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(values, "TNG library: The pointer to the values array must not be a NULL pointer"); TNG_ASSERT(data_type, "TNG library: The pointer to the data type of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_frame_number, "TNG library: The pointer to the frame number of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_time, "TNG library: The pointer to the time of the returned data must not be a NULL pointer"); - + frame_set = &tng_data->current_trajectory_frame_set; - + stat = tng_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { @@ -15404,7 +15475,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read *retrieved_frame_number = i; if(frame_set->first_frame_time >= 0 && tng_data->time_per_frame >= 0) { - *retrieved_time = frame_set->first_frame_time + + *retrieved_time = frame_set->first_frame_time + (i - frame_set->first_frame) * tng_data->time_per_frame; } @@ -15412,7 +15483,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read { *retrieved_time = 0; } - + if(data->stride_length > 1) { i = (i - data->first_frame_with_data) / data->stride_length; @@ -15421,9 +15492,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read { i = (i - frame_set->first_frame) / data->stride_length; } - + *data_type = data->datatype; - + switch(*data_type) { case TNG_CHAR_DATA: @@ -15438,7 +15509,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read default: size = sizeof(double); } - + data_size = size * data->n_values_per_frame; temp = realloc(*values, data_size); @@ -15450,11 +15521,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read *values = 0; return(TNG_CRITICAL); } - + *values = temp; - + memcpy(*values, (char *)data->values + i * data_size, data_size); - + return(TNG_SUCCESS); } @@ -16395,7 +16466,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); - + return(tng_util_generic_write(tng_data, frame_nr, positions, 3, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_PARTICLE_BLOCK_DATA, |