diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 138 |
1 files changed, 109 insertions, 29 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 9a89b8e..b3bb3e1 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -2060,6 +2060,7 @@ static tng_function_status tng_read_frame_set_block } } free(frame_set->mappings); + frame_set->mappings = 0; frame_set->n_mapping_blocks = 0; } @@ -2730,7 +2731,7 @@ static tng_function_status tng_read_trajectory_mapping_block struct tng_gen_block *block, const tng_hash_mode hash_mode) { - int64_t i, old_n_particles; + int64_t i; int offset = 0; tng_bool same_hash; struct tng_trajectory_frame_set *frame_set = @@ -2815,8 +2816,6 @@ static tng_function_status tng_read_trajectory_mapping_block } offset += sizeof(mapping->num_first_particle); - old_n_particles = mapping->n_particles; - memcpy(&mapping->n_particles, block->block_contents+offset, sizeof(mapping->n_particles)); if(tng_data->endianness_64 != TNG_BIG_ENDIAN_64) @@ -2830,21 +2829,14 @@ static tng_function_status tng_read_trajectory_mapping_block } offset += sizeof(mapping->n_particles); - if(old_n_particles != mapping->n_particles) + mapping->real_particle_numbers = malloc(mapping->n_particles * + sizeof(int64_t)); + if(!mapping->real_particle_numbers) { - if(mapping->real_particle_numbers) - { - free(mapping->real_particle_numbers); - } - mapping->real_particle_numbers = malloc(mapping->n_particles * - sizeof(int64_t)); - if(!mapping->real_particle_numbers) - { - printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__); - tng_block_destroy(block); - return(TNG_CRITICAL); - } + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__); + tng_block_destroy(block); + return(TNG_CRITICAL); } for(i = 0; i < mapping->n_particles; i++) @@ -3491,7 +3483,8 @@ static tng_function_status tng_write_particle_data_block { for(i = n_frames; i--;) { - for(j = num_first_particle; j < n_particles; j++) + for(j = num_first_particle; j < num_first_particle + n_particles; + j++) { for(k = data->n_values_per_frame; k--;) { @@ -3653,7 +3646,7 @@ static tng_function_status tng_write_particle_data_block for(i = 0; i < data->n_frames; i++) { - for(j = num_first_particle; j < n_particles; j++) + for(j = num_first_particle; j < num_first_particle + n_particles; j++) { for(k = 0; k < data->n_values_per_frame; k++) { @@ -5522,6 +5515,88 @@ tng_function_status tng_molecule_destroy(tng_molecule_t molecule) return(TNG_SUCCESS); } +tng_function_status tng_particle_mapping_add + (tng_trajectory_t tng_data, + const int64_t first_particle_number, + const int64_t n_particles, + const int64_t *mapping_table) +{ + int64_t i; + struct tng_particle_mapping *mapping; + struct tng_trajectory_frame_set *frame_set = + &tng_data->current_trajectory_frame_set; + + /* Sanity check of the particle ranges. Split into multiple if + * statements for improved readability */ + for(i=0; i<frame_set->n_mapping_blocks; i++) + { + mapping = &frame_set->mappings[i]; + if(first_particle_number >= mapping->num_first_particle && + first_particle_number < mapping->num_first_particle + + mapping->n_particles) + { + printf("Particle mapping overlap. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(first_particle_number + n_particles >= + mapping->num_first_particle && + first_particle_number + n_particles < + mapping->num_first_particle + mapping->n_particles) + { + printf("Particle mapping overlap. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(mapping->num_first_particle >= first_particle_number && + mapping->num_first_particle < first_particle_number + + n_particles) + { + printf("Particle mapping overlap. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + if(mapping->num_first_particle + mapping->n_particles > + first_particle_number && + mapping->num_first_particle + mapping->n_particles < + first_particle_number + n_particles) + { + printf("Particle mapping overlap. %s: %d\n", __FILE__, __LINE__); + return(TNG_FAILURE); + } + } + + frame_set->n_mapping_blocks++; + + mapping = realloc(frame_set->mappings, sizeof(struct tng_particle_mapping) * + frame_set->n_mapping_blocks); + + if(!mapping) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks, + __FILE__, __LINE__); + return(TNG_CRITICAL); + } + frame_set->mappings = mapping; + + mapping = &frame_set->mappings[frame_set->n_mapping_blocks - 1]; + + mapping->num_first_particle = first_particle_number; + mapping->n_particles = n_particles; + mapping->real_particle_numbers = malloc(sizeof(int64_t) * n_particles); + if(!mapping->real_particle_numbers) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + sizeof(int64_t) * n_particles, __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + for(i=0; i<n_particles; i++) + { + mapping->real_particle_numbers[i] = mapping_table[i]; + } + + return(TNG_SUCCESS); +} + tng_function_status tng_trajectory_init(tng_trajectory_t tng_data) { time_t seconds; @@ -5769,17 +5844,21 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) frame_set->contents.block_names = 0; } - for(i = frame_set->n_mapping_blocks; i--;) + if(frame_set->mappings) { - mapping = &frame_set->mappings[i]; - if(mapping->real_particle_numbers) + for(i = frame_set->n_mapping_blocks; i--;) { - free(mapping->real_particle_numbers); - mapping->real_particle_numbers = 0; + 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; } - free(frame_set->mappings); - frame_set->n_mapping_blocks = 0; if(frame_set->molecule_cnt_list) { @@ -6284,11 +6363,11 @@ static tng_function_status tng_particle_mapping_get_real_particle mapping = &frame_set->mappings[i]; first = mapping->num_first_particle; if(local < first || - local > first + mapping->n_particles) + local >= first + mapping->n_particles) { continue; } - *real = mapping->real_particle_numbers[i-first]; + *real = mapping->real_particle_numbers[local-first]; return(TNG_SUCCESS); } *real = local; @@ -6597,7 +6676,7 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, TNG_NORMAL_WRITE, hash_mode); for(j = 0; j<frame_set->n_particle_data_blocks; j++) { - block.id = frame_set->tr_particle_data[i].block_id; + block.id = frame_set->tr_particle_data[j].block_id; tng_write_particle_data_block(tng_data, &block, j, &frame_set->mappings[i], TNG_NORMAL_WRITE, @@ -6678,6 +6757,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, } } free(frame_set->mappings); + frame_set->mappings = 0; frame_set->n_mapping_blocks = 0; } |