diff options
| -rw-r--r-- | src/lib/tng_io.c | 600 |
1 files changed, 486 insertions, 114 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index efcaaab..222156a 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -352,9 +352,6 @@ struct tng_trajectory { * cannot be trusted to be up-to-date */ int64_t n_trajectory_frame_sets; - /** The number of trajectory blocks in the file */ - int64_t n_trajectory_blocks; - /* These data blocks are non-trajectory data blocks */ /** The number of non-frame dependent particle dependent data blocks */ int n_particle_data_blocks; @@ -1029,6 +1026,383 @@ static tng_function_status tng_block_header_read // return(TNG_SUCCESS); // } */ + +static tng_function_status tng_file_pos_of_end_of_non_trajectory_blocks_get + (tng_trajectory_t tng_data, + int64_t *pos) +{ + int64_t orig_pos, curr_pos; + tng_gen_block_t block; + tng_function_status stat; + + orig_pos = ftell(tng_data->input_file); + + *pos = 0; + curr_pos = 0; + fseek(tng_data->input_file, *pos, SEEK_SET); + + tng_block_init(&block); + while(block->id != TNG_TRAJECTORY_FRAME_SET && curr_pos < tng_data->input_file_len) + { + *pos = curr_pos; + /* Read block headers until a frame set block is found */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos, + __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_FAILURE); + } + fseek(tng_data->input_file, block->block_contents_size, SEEK_CUR); + curr_pos += block->block_contents_size; + } + if(curr_pos == tng_data->input_file_len-1) + { + *pos = curr_pos; + } + + tng_block_destroy(&block); + + fseek(tng_data->input_file, orig_pos, SEEK_SET); + + return(TNG_SUCCESS); +} + +static tng_function_status tng_file_pos_of_subsequent_trajectory_block_get + (tng_trajectory_t tng_data, + int64_t *pos) +{ + int64_t orig_pos, curr_frame_set_pos; + tng_gen_block_t block; + tng_function_status stat; + tng_trajectory_frame_set_t frame_set = + &tng_data->current_trajectory_frame_set; + + orig_pos = ftell(tng_data->input_file); + curr_frame_set_pos = tng_data->current_trajectory_frame_set_input_file_pos; + + *pos = tng_data->first_trajectory_frame_set_input_file_pos; + + if(*pos <= 0) + { + return(TNG_SUCCESS); + } + + fseek(tng_data->input_file, *pos, SEEK_SET); + + tng_block_init(&block); + /* Read block headers first to see that a frame set block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos, + __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_FAILURE); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + /* Read all frame set blocks (not the blocks between them) */ + while(frame_set->next_frame_set_file_pos > 0) + { + fseek(tng_data->input_file, frame_set->next_frame_set_file_pos, SEEK_SET); + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos, + __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + if(stat != TNG_SUCCESS || block->id != TNG_TRAJECTORY_FRAME_SET) + { + return(TNG_FAILURE); + } + + stat = tng_block_read_next(tng_data, block, TNG_SKIP_HASH); + if(stat != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(stat); + } + /* Update *pos if this is the earliest frame set so far (after orig_pos) */ + if(tng_data->current_trajectory_frame_set_input_file_pos < *pos && + tng_data->current_trajectory_frame_set_input_file_pos > orig_pos) + { + *pos = tng_data->current_trajectory_frame_set_input_file_pos; + } + } + + /* Re-read the frame set that used to be the current one */ + fseek(tng_data->input_file, curr_frame_set_pos, SEEK_SET); + if(curr_frame_set_pos > 0) + { + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos, + __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_FAILURE); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + + tng_block_destroy(&block); + + fseek(tng_data->input_file, orig_pos, SEEK_SET); + + return(TNG_SUCCESS); +} + +static tng_function_status tng_file_block_migrate(tng_trajectory_t tng_data, + int64_t block_start_pos, + int64_t block_len, + int64_t new_pos) +{ + int64_t i; + + char *contents; + + if(tng_input_file_init(tng_data) != TNG_SUCCESS) + { + return(TNG_CRITICAL); + } + + contents = malloc(block_len); + if(!contents) + { + fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + block_len, __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + /* First read the header size to be able to read the whole header. */ + if(fread(contents, block_len, 1, tng_data->input_file) == 0) + { + fprintf(stderr, "TNG library: Cannot read data from file when migrating data. %s: %d\n", + __FILE__, __LINE__); + free(contents); + return(TNG_CRITICAL); + } + fseek(tng_data->output_file, new_pos, SEEK_SET); + + if(fwrite(contents, block_len, 1, tng_data->output_file) != 1) + { + fprintf(stderr, "TNG library: Could not write data to file when migrating data. %s: %d\n", + __FILE__, __LINE__); + free(contents); + return(TNG_CRITICAL); + } + + fseek(tng_data->output_file, new_pos, SEEK_SET); + + /* Fill the block with NULL to avoid confusion. */ + for(i = 0; i < block_len; i++) + { + contents[i] = '\0'; + } + /* FIXME: casting block_len to size_t is dangerous */ + fwrite(contents, 1, block_len, tng_data->output_file); + + free(contents); + + return(TNG_SUCCESS); +} + +static tng_function_status tng_length_of_current_frame_set_contents_get + (tng_trajectory_t tng_data, + int64_t *len) +{ + int64_t orig_pos, curr_frame_set_pos; + tng_gen_block_t block; + tng_function_status stat; + + orig_pos = ftell(tng_data->input_file); + curr_frame_set_pos = tng_data->current_trajectory_frame_set_input_file_pos; + + *len = 0; + + fseek(tng_data->input_file, curr_frame_set_pos, SEEK_SET); + + tng_block_init(&block); + /* Read block headers first to see that a frame set block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", + curr_frame_set_pos, __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_FAILURE); + } + + /* Read the headers of all blocks in the frame set (not the actual contents of them) */ + while(stat == TNG_SUCCESS) + { + *len += block->header_contents_size; + fseek(tng_data->input_file, block->block_contents_size, SEEK_CUR); + *len += block->block_contents_size; + stat = tng_block_header_read(tng_data, block); + if(block->id == TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Re-read the frame set that used to be the current one */ + fseek(tng_data->input_file, curr_frame_set_pos, SEEK_SET); + if(curr_frame_set_pos > 0) + { + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", + curr_frame_set_pos, __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_FAILURE); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + + tng_block_destroy(&block); + + fseek(tng_data->input_file, orig_pos, SEEK_SET); + + return(TNG_SUCCESS); +} + +/** Migrate blocks in the file to make room for new data in a block. This + * is required e.g. when adding data to a block or extending strings in a + * block. + * @param tng_data is a trajectory data container. + * @param start_pos is the position from which to start moving data, usually + * the byte after the end of the block to which data was added. + * @param offset is the number of bytes that were inserted. + * @details Trajectory blocks (frame sets and their related blocks) are moved + * to the end of the file (if needed) in order to make room for non-trajectory + * data. + */ +static tng_function_status tng_migrate_data_in_file + (tng_trajectory_t tng_data, + int64_t start_pos, + int64_t offset) +{ + int64_t non_traj_end_pos, traj_start_pos, empty_space, orig_file_pos, frame_set_length; + tng_gen_block_t block; + tng_function_status stat; + tng_bool do_migrate_non_trajectroy_blocks = TNG_FALSE, do_migrate_trajectroy_blocks = TNG_FALSE; + FILE *temp; + + temp = tng_data->input_file; + + stat = tng_file_pos_of_end_of_non_trajectory_blocks_get(tng_data, + &non_traj_end_pos); + if(stat != TNG_SUCCESS) + { + tng_data->input_file = temp; + return(stat); + } + + if(non_traj_end_pos < start_pos) + { + fseek(tng_data->input_file, start_pos, SEEK_SET); + } + else + { + do_migrate_non_trajectroy_blocks = TNG_TRUE; + } + + stat = tng_file_pos_of_subsequent_trajectory_block_get(tng_data, &traj_start_pos); + if(stat != TNG_SUCCESS) + { + tng_data->input_file = temp; + return(stat); + } + + if(do_migrate_trajectroy_blocks) + { + empty_space = traj_start_pos - non_traj_end_pos - 1; + } + else + { + empty_space = traj_start_pos - start_pos - 1; + } + + if(empty_space < offset) + { + do_migrate_trajectroy_blocks = TNG_TRUE; + } + + if(do_migrate_trajectroy_blocks) + { + orig_file_pos = ftell(tng_data->input_file); + + while(empty_space < offset) + { + fseek(tng_data->input_file, traj_start_pos, SEEK_SET); + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL) + { + fprintf(stderr, "TNG library: Cannot read block header. %s: %d\n", + __FILE__, __LINE__); + tng_block_destroy(&block); + tng_data->input_file = temp; + return(TNG_CRITICAL); + } + if(stat != TNG_SUCCESS || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_data->input_file = temp; + return(TNG_FAILURE); + } + stat = tng_length_of_current_frame_set_contents_get(tng_data, &frame_set_length); + if(stat != TNG_SUCCESS) + { + tng_data->input_file = temp; + return(stat); + } + stat = tng_file_block_migrate(tng_data, traj_start_pos, + frame_set_length, tng_data->input_file_len); + if(stat != TNG_SUCCESS) + { + tng_data->input_file = temp; + return(stat); + } + } + fseek(tng_data->input_file, orig_file_pos, SEEK_SET); + } + if(do_migrate_non_trajectroy_blocks) + { + stat = tng_file_block_migrate(tng_data, start_pos, non_traj_end_pos, traj_start_pos+offset); + if(stat != TNG_SUCCESS) + { + tng_data->input_file = temp; + return(stat); + } + } + + return(TNG_SUCCESS); +} + /** Write the header of a data block, regardless of its type * @param tng_data is a trajectory data container. * @param block is a general block container. @@ -2175,7 +2549,7 @@ static tng_function_status tng_molecules_block_read if(tng_data->molecules) { - for(i=tng_data->n_molecules; i--;) + for(i=0; i<tng_data->n_molecules; i++) { tng_molecule_destroy(tng_data, &tng_data->molecules[i]); } @@ -2403,7 +2777,7 @@ static tng_function_status tng_molecules_block_read if(molecule->n_chains > 0) { /* Read the chains of the molecule */ - for(j=molecule->n_chains; j--;) + for(j=0; j<molecule->n_chains; j++) { chain->molecule = molecule; @@ -2413,7 +2787,7 @@ static tng_function_status tng_molecules_block_read residue = chain->residues; /* Read the residues of the chain */ - for(k=chain->n_residues; k--;) + for(k=0; k<chain->n_residues; k++) { residue->chain = chain; @@ -2421,7 +2795,7 @@ static tng_function_status tng_molecules_block_read residue->atoms_offset = atom - molecule->atoms; /* Read the atoms of the residue */ - for(l=residue->n_atoms; l--;) + for(l=0; l<residue->n_atoms; l++) { atom->residue = residue; @@ -2438,7 +2812,7 @@ static tng_function_status tng_molecules_block_read { if(molecule->n_residues > 0) { - for(k=molecule->n_residues; k--;) + for(k=0; k<molecule->n_residues; k++) { residue->chain = 0; @@ -2446,7 +2820,7 @@ static tng_function_status tng_molecules_block_read residue->atoms_offset = atom - molecule->atoms; /* Read the atoms of the residue */ - for(l=residue->n_atoms; l--;) + for(l=0; l<residue->n_atoms; l++) { atom->residue = residue; @@ -2459,7 +2833,7 @@ static tng_function_status tng_molecules_block_read } else { - for(l=molecule->n_atoms; l--;) + for(l=0; l<molecule->n_atoms; l++) { atom->residue = 0; @@ -2513,7 +2887,7 @@ static tng_function_status tng_molecules_block_read bond = molecule->bonds; - for(j=molecule->n_bonds; j--;) + for(j=0; j<molecule->n_bonds; j++) { memcpy(&bond->from_atom_id, block->block_contents+offset, sizeof(bond->from_atom_id)); @@ -2598,7 +2972,7 @@ static tng_function_status tng_molecules_block_write len += tng_min_i((int)strlen(molecule->name) + 1, TNG_MAX_STR_LEN); chain = molecule->chains; - for(j = molecule->n_chains; j--;) + for(j = 0; j < molecule->n_chains; j++) { len += sizeof(chain->id); @@ -2621,7 +2995,7 @@ static tng_function_status tng_molecules_block_write } residue = molecule->residues; - for(j = molecule->n_residues; j--;) + for(j = 0; j < molecule->n_residues; j++) { len += sizeof(residue->id); @@ -2644,7 +3018,7 @@ static tng_function_status tng_molecules_block_write } atom = molecule->atoms; - for(j = molecule->n_atoms; j--;) + for(j = 0; j < molecule->n_atoms; j++) { len += sizeof(atom->id); if(!atom->name) @@ -2676,7 +3050,7 @@ static tng_function_status tng_molecules_block_write atom++; } - for(j = molecule->n_bonds; j--;) + for(j = 0; j < molecule->n_bonds; j++) { len += sizeof(bond->from_atom_id) + sizeof(bond->to_atom_id); } @@ -2834,17 +3208,17 @@ static tng_function_status tng_molecules_block_write if(molecule->n_chains > 0) { chain = molecule->chains; - for(j = molecule->n_chains; j--;) + for(j = 0; j < molecule->n_chains; j++) { tng_chain_data_write(tng_data, block, chain, &offset); residue = chain->residues; - for(k = chain->n_residues; k--;) + for(k = 0; k < chain->n_residues; k++) { tng_residue_data_write(tng_data, block, residue, &offset); atom = molecule->atoms + residue->atoms_offset; - for(l = residue->n_atoms; l--;) + for(l = 0; l < residue->n_atoms; l++) { tng_atom_data_write(tng_data, block, atom, &offset); @@ -2860,12 +3234,12 @@ static tng_function_status tng_molecules_block_write if(molecule->n_residues > 0) { residue = molecule->residues; - for(k = molecule->n_residues; k--;) + for(k = 0; k < chain->n_residues; k++) { tng_residue_data_write(tng_data, block, residue, &offset); atom = molecule->atoms + residue->atoms_offset; - for(l = residue->n_atoms; l--;) + for(l = 0; l < residue->n_atoms; l++) { tng_atom_data_write(tng_data, block, atom, &offset); @@ -2877,7 +3251,7 @@ static tng_function_status tng_molecules_block_write else { atom = molecule->atoms; - for(l = molecule->n_atoms; l--;) + for(l = 0; l < molecule->n_atoms; l++) { tng_atom_data_write(tng_data, block, atom, &offset); @@ -2901,7 +3275,7 @@ static tng_function_status tng_molecules_block_write offset += sizeof(molecule->n_bonds); bond = molecule->bonds; - for(j = molecule->n_bonds; j--;) + for(j = 0; j < molecule->n_bonds; j++) { memcpy(block->block_contents+offset, &bond->from_atom_id, sizeof(bond->from_atom_id)); @@ -4360,11 +4734,11 @@ static tng_function_status tng_allocate_particle_data_mem if(data->strings && data->datatype == TNG_CHAR_DATA) { - for(i = data->n_frames; i--;) + for(i = 0; i < data->n_frames; i++) { - for(j = n_particles; j--;) + for(j = 0; j < n_particles; j++) { - for(k = data->n_values_per_frame; k--;) + for(k = 0; k < data->n_values_per_frame; k++) { if(data->strings[i][j][k]) { @@ -4386,7 +4760,7 @@ static tng_function_status tng_allocate_particle_data_mem if(data->datatype == TNG_CHAR_DATA) { data->strings = malloc(sizeof(char ***) * frame_alloc); - for(i = frame_alloc; i-- ;) + for(i = 0; i < frame_alloc; i++) { data->strings[i] = malloc(sizeof(char **) * n_particles); @@ -4397,7 +4771,7 @@ static tng_function_status tng_allocate_particle_data_mem __FILE__, __LINE__); return(TNG_CRITICAL); } - for(j = n_particles; j--;) + for(j = 0; j < n_particles; j++) { data->strings[i][j] = malloc(sizeof(char *) * n_values_per_frame); @@ -4408,7 +4782,7 @@ static tng_function_status tng_allocate_particle_data_mem __FILE__, __LINE__); return(TNG_CRITICAL); } - for(k = n_values_per_frame; k--;) + for(k = 0; k < n_values_per_frame; k++) { data->strings[i][j][k] = 0; } @@ -4471,7 +4845,7 @@ static tng_function_status tng_particle_data_find block_index = -1; if(block_type_flag == TNG_TRAJECTORY_BLOCK) { - for(i = frame_set->n_particle_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_particle_data_blocks; i++) { *data = &frame_set->tr_particle_data[i]; if((*data)->block_id == id) @@ -4483,7 +4857,7 @@ static tng_function_status tng_particle_data_find } else { - for(i = tng_data->n_particle_data_blocks; i-- ;) + for(i = 0; i < tng_data->n_particle_data_blocks; i++) { *data = &tng_data->non_tr_particle_data[i]; if((*data)->block_id == id) @@ -4523,7 +4897,7 @@ static tng_function_status tng_data_find block_index = -1; if(block_type_flag == TNG_TRAJECTORY_BLOCK) { - for(i = frame_set->n_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_data_blocks; i++) { *data = &frame_set->tr_data[i]; if((*data)->block_id == id) @@ -4534,7 +4908,7 @@ static tng_function_status tng_data_find } if(block_index == -1) { - for(i = tng_data->n_data_blocks; i-- ;) + for(i = 0; i < tng_data->n_data_blocks; i++) { *data = &tng_data->non_tr_data[i]; if((*data)->block_id == id) @@ -4547,7 +4921,7 @@ static tng_function_status tng_data_find } else { - for(i = tng_data->n_data_blocks; i-- ;) + for(i = 0; i < tng_data->n_data_blocks; i++) { *data = &tng_data->non_tr_data[i]; if((*data)->block_id == id) @@ -5012,14 +5386,14 @@ static tng_function_status tng_particle_data_block_write if(data->datatype == TNG_CHAR_DATA) { - for(i = n_frames; i--;) + for(i = 0; i < n_frames; i++) { first_dim_values = data->strings[i]; for(j = num_first_particle; j < num_first_particle + n_particles; j++) { second_dim_values = first_dim_values[j]; - for(k = data->n_values_per_frame; k--;) + for(k = 0; k < data->n_values_per_frame; k++) { block->block_contents_size += strlen(second_dim_values[k]) + 1; @@ -5466,9 +5840,9 @@ static tng_function_status tng_allocate_data_mem if(data->strings && data->datatype == TNG_CHAR_DATA) { - for(i = data->n_frames; i--;) + for(i = 0; i < data->n_frames; i++) { - for(j = data->n_values_per_frame; j--;) + for(j = 0; j < data->n_values_per_frame; j++) { if(data->strings[i][j]) { @@ -5490,7 +5864,7 @@ static tng_function_status tng_allocate_data_mem if(data->datatype == TNG_CHAR_DATA) { data->strings = malloc(sizeof(char **) * frame_alloc); - for(i = frame_alloc; i-- ;) + for(i = 0; i < frame_alloc; i++) { data->strings[i] = malloc(sizeof(char *) * n_values_per_frame); if(!data->strings[i]) @@ -5500,7 +5874,7 @@ static tng_function_status tng_allocate_data_mem __FILE__, __LINE__); return(TNG_CRITICAL); } - for(j = n_values_per_frame; j--;) + for(j = 0; j < n_values_per_frame; j++) { data->strings[i][j] = 0; } @@ -5925,9 +6299,9 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, if(data->datatype == TNG_CHAR_DATA) { - for(i = n_frames; i--;) + for(i = 0; i < n_frames; i++) { - for(j = data->n_values_per_frame; j--;) + for(j = 0; j < data->n_values_per_frame; j++) { block->block_contents_size += strlen(data->strings[i][j]) + 1; } @@ -7238,7 +7612,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add while(found_id) { found_id = TNG_FALSE; - for(i = tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { if(tng_data->molecules[i].id == id) { @@ -7308,7 +7682,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add /* FIXME: Should this be a function argument instead? */ tng_data->molecule_cnt_list[tng_data->n_molecules] = 0; - for(i = tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { if(tng_data->molecules[i].id == id) { @@ -7341,7 +7715,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_existing_add while(found_id) { found_id = TNG_FALSE; - for(i = tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { if(tng_data->molecules[i].id == id) { @@ -7471,7 +7845,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(cnt, "TNG library: cnt must not be a NULL pointer."); - for(i = tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { if(&tng_data->molecules[i] == molecule) { @@ -7497,7 +7871,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - for(i = tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { if(&tng_data->molecules[i] == molecule) { @@ -7891,7 +8265,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add (*chain)->molecule = molecule; (*chain)->n_residues = 0; - for(i = molecule->n_chains; i--;) + for(i = 0; i < molecule->n_chains; i++) { if(molecule->chains[i].id == id) { @@ -8196,7 +8570,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add (*residue)->n_atoms = 0; (*residue)->atoms_offset = 0; - for(i = chain->n_residues; i--;) + for(i = 0; i < chain->n_residues; i++) { if(chain->residues[i].id == id) { @@ -8375,7 +8749,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add (*atom)->residue = residue; - for(i = molecule->n_atoms; i--;) + for(i = 0; i < molecule->n_atoms; i++) { if(molecule->atoms[i].id == id) { @@ -8457,7 +8831,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_ if(molecule->chains) { - for(i = molecule->n_chains; i--;) + for(i = 0; i < molecule->n_chains; i++) { if(molecule->chains[i].name) { @@ -8472,7 +8846,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_ if(molecule->residues) { - for(i = molecule->n_residues; i--;) + for(i = 0; i < molecule->n_residues; i++) { if(molecule->residues[i].name) { @@ -8487,7 +8861,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_ if(molecule->atoms) { - for(i = molecule->n_atoms; i--;) + for(i = 0; i < molecule->n_atoms; i++) { tng_atom_destroy(&molecule->atoms[i]); } @@ -9060,7 +9434,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(tng_tr if(frame_set->n_mapping_blocks && frame_set->mappings) { - for(i = frame_set->n_mapping_blocks; i--;) + for(i = 0; i < frame_set->n_mapping_blocks; i++) { mapping = &frame_set->mappings[i]; if(mapping->real_particle_numbers) @@ -9130,7 +9504,6 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_ tng_data->current_trajectory_frame_set_output_file_pos = -1; tng_data->frame_set_n_frames = 100; tng_data->n_trajectory_frame_sets = 0; - tng_data->n_trajectory_blocks = 0; tng_data->medium_stride_length = 100; tng_data->long_stride_length = 10000; @@ -9359,7 +9732,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t if(tng_data->non_tr_particle_data) { - for(i = tng_data->n_particle_data_blocks; i--; ) + for(i = 0; i < tng_data->n_particle_data_blocks; i++) { if(tng_data->non_tr_particle_data[i].values) { @@ -9373,11 +9746,11 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t n_values_per_frame; if(tng_data->non_tr_particle_data[i].strings[0]) { - for(j = n_particles; j--;) + for(j = 0; j < n_particles; j++) { if(tng_data->non_tr_particle_data[i].strings[0][j]) { - for(k = n_values_per_frame; k--;) + for(k = 0; k < n_values_per_frame; k++) { if(tng_data->non_tr_particle_data[i]. strings[0][j][k]) @@ -9412,7 +9785,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t if(tng_data->non_tr_data) { - for(i = tng_data->n_data_blocks; i--;) + for(i = 0; i < tng_data->n_data_blocks; i++) { if(tng_data->non_tr_data[i].values) { @@ -9426,7 +9799,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t n_values_per_frame; if(tng_data->non_tr_data[i].strings[0]) { - for(j = n_values_per_frame; j--;) + for(j = 0; j < n_values_per_frame; j++) { if(tng_data->non_tr_data[i].strings[0][j]) { @@ -9467,7 +9840,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t if(frame_set->tr_particle_data) { - for(i = frame_set->n_particle_data_blocks; i--; ) + for(i = 0; i < frame_set->n_particle_data_blocks; i++) { if(frame_set->tr_particle_data[i].values) { @@ -9479,16 +9852,16 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t { n_values_per_frame = frame_set->tr_particle_data[i]. n_values_per_frame; - for(j = frame_set->tr_particle_data[i].n_frames; j--;) + for(j = 0; j < frame_set->tr_particle_data[i].n_frames; j++) { if(frame_set->tr_particle_data[i].strings[j]) { - for(k = n_particles; k--;) + for(k = 0; k < n_particles; k++) { if(frame_set->tr_particle_data[i]. strings[j][k]) { - for(l = n_values_per_frame; l--;) + for(l = 0; l < n_values_per_frame; l++) { if(frame_set->tr_particle_data[i]. strings[j][k][l]) @@ -9525,7 +9898,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t if(frame_set->tr_data) { - for(i = frame_set->n_data_blocks; i--;) + for(i = 0; i < frame_set->n_data_blocks; i++) { if(frame_set->tr_data[i].values) { @@ -9537,11 +9910,11 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t { n_values_per_frame = frame_set->tr_data[i]. n_values_per_frame; - for(j = frame_set->tr_data[i].n_frames; j--;) + for(j = 0; j < frame_set->tr_data[i].n_frames; j++) { if(frame_set->tr_data[i].strings[j]) { - for(k = n_values_per_frame; k--;) + for(k = 0; k < n_values_per_frame; k++) { if(frame_set->tr_data[i].strings[j][k]) { @@ -9572,7 +9945,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t if(tng_data->molecules) { - for(i=tng_data->n_molecules; i--;) + for(i = 0; i < tng_data->n_molecules; i++) { tng_molecule_destroy(tng_data, &tng_data->molecules[i]); } @@ -9657,7 +10030,6 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector src->current_trajectory_frame_set_output_file_pos; dest->frame_set_n_frames = src->frame_set_n_frames; dest->n_trajectory_frame_sets = src->n_trajectory_frame_sets; - dest->n_trajectory_blocks = src->n_trajectory_blocks; dest->medium_stride_length = src->medium_stride_length; dest->long_stride_length = src->long_stride_length; @@ -10796,7 +11168,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get return(TNG_FAILURE); } - for(i = tng_data->n_molecules; i --;) + for(i = 0; i < tng_data->n_molecules; i++) { cnt += cnt_list[i]; } @@ -11137,7 +11509,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find } if(tng_block_read_next(tng_data, block, - TNG_SKIP_HASH) != TNG_SUCCESS) + TNG_SKIP_HASH) != TNG_SUCCESS) { tng_block_destroy(&block); return(TNG_CRITICAL); @@ -14284,7 +14656,7 @@ static tng_function_status tng_data_values_alloc } - for(i = n_frames; i--;) + for(i = 0; i < n_frames; i++) { (*values)[i] = malloc(sizeof(union data_values) * n_values_per_frame); @@ -14320,7 +14692,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_values_free { if(type == TNG_CHAR_DATA) { - for(j = n_values_per_frame; j--;) + for(j = 0; j < n_values_per_frame; j++) { if(values[i][j].c) { @@ -14378,7 +14750,7 @@ static tng_function_status tng_particle_data_values_alloc } - for(i = n_frames; i--;) + for(i = 0; i < n_frames; i++) { (*values)[i] = malloc(sizeof(union data_values *) * n_particles); @@ -14391,7 +14763,7 @@ static tng_function_status tng_particle_data_values_alloc *values = 0; return(TNG_CRITICAL); } - for(j = n_particles; j--;) + for(j = 0; j < n_particles; j++) { (*values)[i][j] = malloc(sizeof(union data_values) * n_values_per_frame); @@ -14433,7 +14805,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free { if(type == TNG_CHAR_DATA) { - for(k = n_values_per_frame; k--;) + for(k = 0; k < n_values_per_frame; k++) { if(values[i][j][k].c) { @@ -14513,7 +14885,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get return(stat); } - for(i = frame_set->n_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_data_blocks; i++) { data = &frame_set->tr_data[i]; if(data->block_id == block_id) @@ -14546,9 +14918,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get switch(*type) { case TNG_CHAR_DATA: - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { len = strlen(data->strings[i][j]) + 1; (*values)[i][j].c = malloc(len); @@ -14558,9 +14930,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get break; case TNG_INT_DATA: size = sizeof(int); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].i = *(int *)((char *)data->values + size * (i*(*n_values_per_frame) + j)); @@ -14569,9 +14941,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get break; case TNG_FLOAT_DATA: size = sizeof(float); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].f = *(float *)((char *)data->values + size * (i*(*n_values_per_frame) + j)); @@ -14581,9 +14953,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get case TNG_DOUBLE_DATA: default: size = sizeof(double); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].d = *(double *)((char *)data->values + size * (i*(*n_values_per_frame) + j)); @@ -14653,7 +15025,7 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, return(stat); } - for(i = frame_set->n_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_data_blocks; i++) { data = &frame_set->tr_data[i]; if(data->block_id == block_id) @@ -14784,7 +15156,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get /* See if there is a data block of this ID. * Start checking the last read frame set */ - for(i = frame_set->n_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_data_blocks; i++) { data = &frame_set->tr_data[i]; if(data->block_id == block_id) @@ -14833,7 +15205,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } current_frame_pos = 0; } - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { len = strlen(data->strings[current_frame_pos][j]) + 1; (*values)[i][j].c = malloc(len); @@ -14855,7 +15227,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } current_frame_pos = 0; } - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].i = *(int *)((char *)data->values + size * (current_frame_pos * @@ -14877,7 +15249,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } current_frame_pos = 0; } - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].f = *(float *)((char *)data->values + size * (current_frame_pos * @@ -14900,7 +15272,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get } current_frame_pos = 0; } - for(j=*n_values_per_frame; j--;) + for(j = 0; j < *n_values_per_frame; j++) { (*values)[i][j].d = *(double *)((char *)data->values + size * (current_frame_pos * @@ -15223,7 +15595,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get return(stat); } - for(i = frame_set->n_particle_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_particle_data_blocks; i++) { data = &frame_set->tr_particle_data[i]; if(data->block_id == block_id) @@ -15281,12 +15653,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get switch(*type) { case TNG_CHAR_DATA: - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { len = strlen(data->strings[i][j][k]) + 1; (*values)[i][mapping][k].c = malloc(len); @@ -15299,12 +15671,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get case TNG_INT_DATA: size = sizeof(int); i_step = (*n_particles) * (*n_values_per_frame); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { (*values)[i][mapping][k].i = *(int *) ((char *)data->values + size * @@ -15317,12 +15689,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get case TNG_FLOAT_DATA: size = sizeof(float); i_step = (*n_particles) * (*n_values_per_frame); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { (*values)[i][mapping][k].f = *(float *) ((char *)data->values + size * @@ -15336,12 +15708,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get default: size = sizeof(double); i_step = (*n_particles) * (*n_values_per_frame); - for(i=*n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { (*values)[i][mapping][k].d = *(double *) ((char *)data->values + size * @@ -15418,7 +15790,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get return(stat); } - for(i = frame_set->n_particle_data_blocks; i-- ;) + for(i = 0; i < frame_set->n_particle_data_blocks; i++) { data = &frame_set->tr_particle_data[i]; if(data->block_id == block_id) @@ -15499,9 +15871,9 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get else { i_step = (*n_particles) * (*n_values_per_frame); - for(i = *n_frames; i--;) + for(i = 0; i < *n_frames; i++) { - for(j = *n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); memcpy(((char *)*values) + size * (i * i_step + mapping * @@ -15651,10 +16023,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } current_frame_pos = 0; } - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { len = strlen(data->strings[current_frame_pos][j][k]) + 1; (*values)[i][mapping][k].c = malloc(len); @@ -15678,10 +16050,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } current_frame_pos = 0; } - for(j=*n_particles; j--;) + for(j = 0; j < *n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k = 0; k < *n_values_per_frame; k++) { (*values)[i][mapping][k].i = *(int *) ((char *)data->values + size * @@ -15707,10 +16079,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } current_frame_pos = 0; } - for(j=*n_particles; j--;) + for(j=0; j<*n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k=0; k<*n_values_per_frame; k++) { (*values)[i][mapping][k].f = *(float *) ((char *)data->values + size * @@ -15737,10 +16109,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get } current_frame_pos = 0; } - for(j=*n_particles; j--;) + for(j=0; j<*n_particles; j++) { tng_particle_mapping_get_real_particle(frame_set, j, &mapping); - for(k=*n_values_per_frame; k--;) + for(k=0; k<*n_values_per_frame; k++) { (*values)[i][mapping][k].d = *(double *) ((char *)data->values + size * |