diff options
| -rw-r--r-- | include/tng_io.h | 15 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 73 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 2 |
3 files changed, 52 insertions, 38 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index b6d0890..3b19a32 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -2323,6 +2323,19 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add const int64_t *mapping_table); /** + * @brief Remove all particle mappings (in memory) from the current frame set. + * @details Clears the currently setup particle mappings of the current frame + * set. + * @param tng_data is the trajectory, with the frame set of which to clear + * all particle mappings. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @return TNG_SUCCESS (0) if successful. + */ +tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free + (tng_trajectory_t tng_data); + +/** * @brief Read the header blocks from the input_file of tng_data. * @details The trajectory blocks must be read separately and iteratively in chunks * to fit in memory. @@ -2504,6 +2517,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_premature_write /** * @brief Create and initialise a frame set. + * @details Particle mappings are retained from previous frame set (if any). + * To explicitly clear particle mappings use tng_frame_set_particle_mapping_free(). * @param tng_data is the trajectory data container in which to add the frame * set. * @param first_frame is the first frame of the frame set. diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 4611037..e4774dd 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -722,35 +722,6 @@ static tng_function_status tng_output_file_init(tng_trajectory_t tng_data) return(TNG_SUCCESS); } -static tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(tng_trajectory_t tng_data) -{ - tng_trajectory_frame_set_t frame_set; - tng_particle_mapping_t mapping; - int64_t i; - - TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - - frame_set = &tng_data->current_trajectory_frame_set; - - if(frame_set->n_mapping_blocks && frame_set->mappings) - { - for(i = frame_set->n_mapping_blocks; i--;) - { - mapping = &frame_set->mappings[i]; - if(mapping->real_particle_numbers) - { - free(mapping->real_particle_numbers); - mapping->real_particle_numbers = 0; - } - } - free(frame_set->mappings); - frame_set->mappings = 0; - frame_set->n_mapping_blocks = 0; - } - - return(TNG_SUCCESS); -} - /** Setup a file block container. * @param block_p a pointer to memory to initialise as a file block container. * @details Memory is allocated during initialisation. @@ -7446,7 +7417,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set { old_cnt = tng_data->current_trajectory_frame_set.molecule_cnt_list[index]; tng_data->current_trajectory_frame_set.molecule_cnt_list[index] = cnt; - + tng_data->current_trajectory_frame_set.n_particles += (cnt-old_cnt) * tng_data->molecules[index].n_atoms; } @@ -8443,7 +8414,7 @@ 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); @@ -8550,7 +8521,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get { return(TNG_SUCCESS); } - + *from_atoms = malloc(sizeof(int64_t) * (*n_bonds)); if(!*from_atoms) { @@ -8971,6 +8942,35 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(tng_trajectory_t tng_data) +{ + tng_trajectory_frame_set_t frame_set; + tng_particle_mapping_t mapping; + int64_t i; + + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + + frame_set = &tng_data->current_trajectory_frame_set; + + if(frame_set->n_mapping_blocks && frame_set->mappings) + { + for(i = frame_set->n_mapping_blocks; i--;) + { + mapping = &frame_set->mappings[i]; + if(mapping->real_particle_numbers) + { + free(mapping->real_particle_numbers); + mapping->real_particle_numbers = 0; + } + } + free(frame_set->mappings); + frame_set->mappings = 0; + frame_set->n_mapping_blocks = 0; + } + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_data_p) { time_t seconds; @@ -10561,7 +10561,7 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set tng_molecule_cnt_get(tng_data, mol, &n_impl); diff -= n_impl * mol->n_atoms; } - + if(diff == 0) { if(stat == TNG_SUCCESS) @@ -12354,9 +12354,6 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new tng_data->current_trajectory_frame_set_output_file_pos = ftell(tng_data->output_file); - /* Clear mappings if they remain. */ - tng_frame_set_particle_mapping_free(tng_data); - tng_data->n_trajectory_frame_sets++; /* Set the medium range pointers */ @@ -14849,7 +14846,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get __FILE__, __LINE__); return(stat); } - + fseek(tng_data->input_file, (long)block->block_contents_size, SEEK_CUR); } file_pos = ftell(tng_data->input_file); @@ -15693,7 +15690,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get __FILE__, __LINE__); return(stat); } - + fseek(tng_data->input_file, (long)block->block_contents_size, SEEK_CUR); } file_pos = ftell(tng_data->input_file); diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index ff41024..3899b15 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -286,6 +286,8 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t *traj) return(TNG_CRITICAL); } + tng_frame_set_particle_mapping_free(*traj); + /* Setup particle mapping. Use 4 different mapping blocks with arbitrary * mappings. */ for(k=0; k<150; k++) |