diff options
Diffstat (limited to 'src/lib/tng_io.c')
| -rw-r--r-- | src/lib/tng_io.c | 418 |
1 files changed, 272 insertions, 146 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 14bdfed..3be1863 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -5435,8 +5435,8 @@ tng_function_status tng_trajectory_init(tng_trajectory_t tng_data) tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) { - int64_t n_frames, n_particles; - int i, j, k, l; + int64_t n_particles; + int i; struct tng_trajectory_frame_set *frame_set = &tng_data->current_trajectory_frame_set; @@ -5547,45 +5547,16 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) { for(i = tng_data->n_particle_data_blocks; i--; ) { - if(tng_data->non_tr_particle_data[i].values) - { - /* Only one frame for non-trajectory data */ - j = 0; - if(tng_data->non_tr_particle_data[i].values[j]) - { - for(k = n_particles; k--;) - { - if(tng_data->non_tr_particle_data[i].values[j][k]) - { - if(tng_data->non_tr_particle_data[i].datatype == - TNG_CHAR_DATA) - { - for(l = tng_data->non_tr_particle_data[i]. - n_values_per_frame; - l--;) - { - if(tng_data->non_tr_particle_data[i]. - values[j][k][l].c) - { - free(tng_data->non_tr_particle_data[i]. - values[j][k][l].c); - tng_data->non_tr_particle_data[i]. - values[j][k][l].c = 0; - } - } - } - free(tng_data->non_tr_particle_data[i]. - values[j][k]); - tng_data->non_tr_particle_data[i]. - values[j][k] = 0; - } - } - free(tng_data->non_tr_particle_data[i].values[j]); - tng_data->non_tr_particle_data[i].values[j] = 0; - } - free(tng_data->non_tr_particle_data[i].values); - tng_data->non_tr_particle_data[i].values = 0; - } + tng_particle_data_values_free(tng_data->non_tr_particle_data[i]. + values, + tng_data->non_tr_particle_data[i]. + n_frames, + n_particles, + tng_data->non_tr_particle_data[i]. + n_values_per_frame, + tng_data->non_tr_particle_data[i]. + datatype); + if(tng_data->non_tr_particle_data[i].block_name) { free(tng_data->non_tr_particle_data[i].block_name); @@ -5600,30 +5571,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) { for(i = tng_data->n_data_blocks; i--;) { - if(tng_data->non_tr_data[i].values) - { - /* Only one frame for non-trajectory data */ - if(tng_data->non_tr_data[i].values[0]) - { - if(tng_data->non_tr_data[i].datatype == - TNG_CHAR_DATA) - { - for(k = tng_data->non_tr_data[i].n_values_per_frame; - k--;) - { - if(tng_data->non_tr_data[i].values[0][k].c) - { - free(tng_data->non_tr_data[i].values[0][k].c); - tng_data->non_tr_data[i].values[0][k].c = 0; - } - } - } - free(tng_data->non_tr_data[i].values[0]); - tng_data->non_tr_data[i].values[0] = 0; - } - free(tng_data->non_tr_data[i].values); - tng_data->non_tr_data[i].values = 0; - } + tng_data_values_free(tng_data->non_tr_data[i].values, 1, + tng_data->non_tr_data[i].n_values_per_frame, + tng_data->non_tr_data[i].datatype); + if(tng_data->non_tr_data[i].block_name) { free(tng_data->non_tr_data[i].block_name); @@ -5641,47 +5592,16 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) { for(i = frame_set->n_particle_data_blocks; i--; ) { - if(frame_set->tr_particle_data[i].values) - { - n_frames = max(1, frame_set->tr_particle_data[i].n_frames); - for(j = n_frames; j--;) - { - if(frame_set->tr_particle_data[i].values[j]) - { - for(k = n_particles; k--;) - { - if(frame_set->tr_particle_data[i].values[j][k]) - { - if(frame_set->tr_particle_data[i].datatype == - TNG_CHAR_DATA) - { - for(l = frame_set->tr_particle_data[i]. - n_values_per_frame; - l--;) - { - if(frame_set->tr_particle_data[i]. - values[j][k][l].c) - { - free(frame_set->tr_particle_data[i]. - values[j][k][l].c); - - frame_set->tr_particle_data[i]. - values[j][k][l].c = 0; - } - } - } - free(frame_set->tr_particle_data[i]. - values[j][k]); - frame_set->tr_particle_data[i].values[j][k] = 0; - } - } - free(frame_set->tr_particle_data[i].values[j]); - frame_set->tr_particle_data[i].values[j] = 0; - } - } - free(frame_set->tr_particle_data[i].values); - frame_set->tr_particle_data[i].values = 0; - } + tng_particle_data_values_free(frame_set->tr_particle_data[i]. + values, + frame_set->tr_particle_data[i]. + n_frames, + n_particles, + frame_set->tr_particle_data[i]. + n_values_per_frame, + frame_set->tr_particle_data[i]. + datatype); + if(frame_set->tr_particle_data[i].block_name) { free(frame_set->tr_particle_data[i].block_name); @@ -5696,36 +5616,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data) { for(i = frame_set->n_data_blocks; i--;) { - if(frame_set->tr_data[i].values) - { - n_frames = max(1, frame_set->tr_data[i].n_frames); - for(j = n_frames; j--;) - { - if(frame_set->tr_data[i].values[j]) - { - if(frame_set->tr_data[i].datatype == - TNG_CHAR_DATA) - { - for(k = frame_set->tr_data[i].n_values_per_frame; - k--;) - { - if(frame_set->tr_data[i].values[j][k].c) - { - free(frame_set->tr_data[i]. - values[j][k].c); - - frame_set->tr_data[i]. - values[j][k].c = 0; - } - } - } - free(frame_set->tr_data[i].values[j]); - frame_set->tr_data[i].values[j] = 0; - } - } - free(frame_set->tr_data[i].values); - frame_set->tr_data[i].values = 0; - } + tng_data_values_free(frame_set->tr_data[i].values, 1, + frame_set->tr_data[i]. + n_values_per_frame, + frame_set->tr_data[i].datatype); if(frame_set->tr_data[i].block_name) { free(frame_set->tr_data[i].block_name); @@ -6887,13 +6781,90 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, return(TNG_SUCCESS); } +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) +{ + int i, j; + + if(values) + { + for(i = 0; i < n_frames; i++) + { + if(values[i]) + { + if(type == TNG_CHAR_DATA) + { + for(j = n_values_per_frame; j--;) + { + if(values[i][j].c) + { + free(values[i][j].c); + values[i][j].c = 0; + } + } + } + free(values[i]); + values[i] = 0; + } + } + free(values); + values = 0; + } + + return(TNG_SUCCESS); +} + +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) +{ + int i, j, k; + if(values) + { + for(i = 0; i < n_frames; i++) + { + if(values[i]) + { + for(j = 0; j < n_particles; j++) + { + if(type == TNG_CHAR_DATA) + { + for(k = n_values_per_frame; k--;) + { + if(values[i][j][k].c) + { + free(values[i][j][k].c); + values[i][j][k].c = 0; + } + } + } + free(values[i][j]); + values[i][j] = 0; + } + free(values[i]); + values[i] = 0; + } + } + free(values); + values = 0; + } + + return(TNG_SUCCESS); +} tng_function_status tng_data_get(tng_trajectory_t tng_data, int64_t block_id, - union data_values ***values) + union data_values ***values, + int64_t *n_frames, + int64_t *n_values_per_frame, + tng_data_type *type) { - int i, block_index; - struct tng_data *data; + int i, j, block_index, len; + struct tng_data *data, *new_data; struct tng_trajectory_frame_set *frame_set = &tng_data->current_trajectory_frame_set; @@ -6929,7 +6900,67 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, } } - *values = data->values; + /* A bit hackish to create a new data struct before returning the data */ + new_data = malloc(sizeof(struct tng_data)); + + new_data->n_values_per_frame = 0; + new_data->n_frames = 0; + new_data->values = 0; + new_data->datatype = data->datatype; + *n_values_per_frame = data->n_values_per_frame; + if(tng_allocate_data_mem(tng_data, new_data, data->n_frames, + *n_values_per_frame) != TNG_SUCCESS) + { + return(TNG_CRITICAL); + } + + *n_frames = max(1, data->n_frames); + + *values = new_data->values; + *type = data->datatype; + switch(*type) + { + case TNG_CHAR_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_values_per_frame; j--;) + { + len = strlen(data->values[i][j].c) + 1; + (*values)[i][j].c = malloc(len); + strncpy((*values)[i][j].c, data->values[i][j].c, len); + } + } + break; + case TNG_INT_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].i = data->values[i][j].i; + } + } + break; + case TNG_FLOAT_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].f = data->values[i][j].f; + } + } + break; + case TNG_DOUBLE_DATA: + default: + for(i=*n_frames; i--;) + { + for(j=*n_values_per_frame; j--;) + { + (*values)[i][j].d = data->values[i][j].d; + } + } + } + + free(new_data); return(TNG_SUCCESS); } @@ -6938,7 +6969,9 @@ 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, - union data_values ***values) + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type) { /* STUB */ return(TNG_SUCCESS); @@ -6946,13 +6979,19 @@ 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, - union data_values ****values) + union data_values ****values, + int64_t *n_frames, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type) { - int i, block_index; - struct tng_particle_data *data; + int i, j, k, block_index, len; + struct tng_particle_data *data, *new_data; struct tng_trajectory_frame_set *frame_set = &tng_data->current_trajectory_frame_set; + tng_block_type block_type_flag; + block_index = -1; /* See if there is already a data block of this ID. * Start checking the last read frame set */ @@ -6962,6 +7001,7 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, if(data->block_id == block_id) { block_index = i; + block_type_flag = TNG_TRAJECTORY_BLOCK; break; } } @@ -6976,6 +7016,7 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, if(data->block_id == block_id) { block_index = i; + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; break; } } @@ -6987,7 +7028,90 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, } } - *values = data->values; + if(block_type_flag == TNG_TRAJECTORY_BLOCK && + tng_data->var_num_atoms_flag) + { + *n_particles = frame_set->n_particles; + } + else + { + *n_particles = tng_data->n_particles; + } + + /* A bit hackish to create a new data struct before returning the data */ + new_data = malloc(sizeof(struct tng_particle_data)); + + new_data->n_values_per_frame = 0; + new_data->n_frames = 0; + new_data->values = 0; + new_data->datatype = data->datatype; + *n_values_per_frame = data->n_values_per_frame; + if(tng_allocate_particle_data_mem(tng_data, new_data, data->n_frames, + *n_particles, data->n_values_per_frame) != + TNG_SUCCESS) + { + return(TNG_CRITICAL); + } + + *n_frames = max(1, data->n_frames); + + *values = new_data->values; + *type = data->datatype; + switch(*type) + { + case TNG_CHAR_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_particles; j--;) + { + for(k=*n_values_per_frame; k--;) + { + len = strlen(data->values[i][j][k].c) + 1; + (*values)[i][j][k].c = malloc(len); + strncpy((*values)[i][j][k].c, data->values[i][j][k].c, len); + } + } + } + break; + case TNG_INT_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_particles; j--;) + { + for(k=*n_values_per_frame; k--;) + { + (*values)[i][j][k].i = data->values[i][j][k].i; + } + } + } + break; + case TNG_FLOAT_DATA: + for(i=*n_frames; i--;) + { + for(j=*n_particles; j--;) + { + for(k=*n_values_per_frame; k--;) + { + (*values)[i][j][k].f = data->values[i][j][k].f; + } + } + } + break; + case TNG_DOUBLE_DATA: + default: + for(i=*n_frames; i--;) + { + for(j=*n_particles; j--;) + { + for(k=*n_values_per_frame; k--;) + { + (*values)[i][j][k].d = data->values[i][j][k].d; + } + } + } + } + + free(new_data); return(TNG_SUCCESS); } @@ -6998,7 +7122,9 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, int64_t end_frame_nr, int64_t first_particle_number, int64_t last_particle_number, - union data_values ****values) + union data_values ****values, + int64_t *n_values_per_frame, + tng_data_type *type) { /* STUB */ return(TNG_SUCCESS); |