diff options
| -rw-r--r-- | src/lib/tng_io.c | 482 |
1 files changed, 241 insertions, 241 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 30daf66..0e3d6bd 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -6,7 +6,7 @@ * Copyright (c) 2012, The GROMACS development team. * Check out http://www.gromacs.org for more information. * - * + * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 @@ -588,7 +588,7 @@ static tng_function_status hash_match_verify(tng_gen_block_t block, { *results = TNG_TRUE; } - + return(TNG_SUCCESS); } @@ -596,7 +596,7 @@ static tng_function_status hash_match_verify(tng_gen_block_t block, * @param tng_data is a trajectory data container. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. - */ + */ static tng_function_status tng_input_file_init(tng_trajectory_t tng_data) { if(!tng_data->input_file) @@ -635,7 +635,7 @@ static tng_function_status tng_output_file_init(tng_trajectory_t tng_data) } tng_data->output_file = fopen(tng_data->output_file_path, "w+"); - + if(!tng_data->output_file) { printf("Cannot open file %s. %s: %d\n", @@ -651,7 +651,7 @@ static tng_function_status tng_output_file_init(tng_trajectory_t tng_data) * @details Memory is allocated during initialisation. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. - */ + */ static tng_function_status tng_block_init(struct tng_gen_block **block_p) { // printf("In tng_block_init\n"); @@ -666,9 +666,9 @@ static tng_function_status tng_block_init(struct tng_gen_block **block_p) sizeof(struct tng_gen_block), __FILE__, __LINE__); return(TNG_CRITICAL); } - + block = *block_p; - + block->id = -1; /* Reset the hash */ memcpy(block->hash, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", TNG_HASH_LEN); @@ -697,7 +697,7 @@ static tng_function_status tng_block_destroy(struct tng_gen_block **block_p) { return(TNG_SUCCESS); } - + // printf("Destroying block\n"); if(block->name) { @@ -736,7 +736,7 @@ static tng_function_status tng_block_header_read { return(TNG_CRITICAL); } - + /* First read the header size to be able to read the whole header. */ if(fread(&block->header_contents_size, sizeof(block->header_contents_size), 1, tng_data->input_file) == 0) @@ -875,7 +875,7 @@ static tng_function_status tng_block_header_read } offset += sizeof(block->id); - + memcpy(block->hash, block->header_contents+offset, TNG_HASH_LEN); offset += TNG_HASH_LEN; @@ -974,7 +974,7 @@ static tng_function_status tng_block_header_write __FILE__, __LINE__); return(TNG_CRITICAL); } - + if(!block->name) { @@ -1031,7 +1031,7 @@ static tng_function_status tng_block_header_write } } offset += sizeof(block->header_contents_size); - + memcpy(block->header_contents+offset, &block->block_contents_size, sizeof(block->block_contents_size)); if(tng_data->output_endianness_swap_func_64) @@ -1045,7 +1045,7 @@ static tng_function_status tng_block_header_write } } offset += sizeof(block->block_contents_size); - + memcpy(block->header_contents+offset, &block->id, sizeof(block->id)); if(tng_data->output_endianness_swap_func_64) { @@ -1158,8 +1158,8 @@ static tng_function_status tng_general_info_block_read tng_data->first_program_name = temp; strncpy(tng_data->first_program_name, block->block_contents, len); offset += len; - - len = tng_min(strlen(block->block_contents) + 1, TNG_MAX_STR_LEN); + + len = tng_min(strlen(block->block_contents + offset) + 1, TNG_MAX_STR_LEN); temp = realloc(tng_data->last_program_name, len); if(!temp) { @@ -1184,7 +1184,7 @@ static tng_function_status tng_general_info_block_read tng_data->first_user_name = temp; strncpy(tng_data->first_user_name, block->block_contents+offset, len); offset += len; - + len = tng_min(strlen(block->block_contents+offset) + 1, TNG_MAX_STR_LEN); temp = realloc(tng_data->last_user_name, len); if(!temp) @@ -1294,7 +1294,7 @@ static tng_function_status tng_general_info_block_read } } offset += sizeof(tng_data->frame_set_n_frames); - + memcpy(&tng_data->first_trajectory_frame_set_input_file_pos, block->block_contents+offset, sizeof(tng_data->first_trajectory_frame_set_input_file_pos)); @@ -1309,11 +1309,11 @@ static tng_function_status tng_general_info_block_read } } offset += sizeof(tng_data->first_trajectory_frame_set_input_file_pos); - + tng_data->current_trajectory_frame_set.next_frame_set_file_pos = tng_data->first_trajectory_frame_set_input_file_pos; - - + + memcpy(&tng_data->last_trajectory_frame_set_input_file_pos, block->block_contents+offset, sizeof(tng_data->last_trajectory_frame_set_input_file_pos)); @@ -1355,7 +1355,7 @@ static tng_function_status tng_general_info_block_read __FILE__, __LINE__); } } - + return(TNG_SUCCESS); } @@ -1497,7 +1497,7 @@ static tng_function_status tng_general_info_block_write tng_block_destroy(&block); return(TNG_CRITICAL); } - + strcpy(block->name, "GENERAL INFO"); block->id = TNG_GENERAL_INFO; @@ -1599,7 +1599,7 @@ static tng_function_status tng_general_info_block_write memcpy(block->block_contents+offset, &tng_data->var_num_atoms_flag, sizeof(tng_data->var_num_atoms_flag)); offset += sizeof(tng_data->var_num_atoms_flag); - + memcpy(block->block_contents+offset, &tng_data->frame_set_n_frames, sizeof(tng_data->frame_set_n_frames)); if(tng_data->output_endianness_swap_func_64) @@ -1643,7 +1643,7 @@ static tng_function_status tng_general_info_block_write } } offset += sizeof(tng_data->last_trajectory_frame_set_input_file_pos); - + memcpy(block->block_contents+offset, &tng_data->medium_stride_length, sizeof(tng_data->medium_stride_length)); if(tng_data->output_endianness_swap_func_64) @@ -1688,7 +1688,7 @@ static tng_function_status tng_general_info_block_write } tng_block_destroy(&block); - + return(TNG_SUCCESS); } @@ -1705,7 +1705,7 @@ static tng_function_status tng_chain_data_read(tng_trajectory_t tng_data, int *offset) { int len; - + memcpy(&chain->id, block->block_contents+*offset, sizeof(chain->id)); if(tng_data->input_endianness_swap_func_64) @@ -1757,7 +1757,7 @@ static tng_function_status tng_chain_data_write(tng_trajectory_t tng_data, int *offset) { int len; - + memcpy(block->block_contents+*offset, &chain->id, sizeof(chain->id)); if(tng_data->output_endianness_swap_func_64) { @@ -1805,7 +1805,7 @@ static tng_function_status tng_residue_data_read(tng_trajectory_t tng_data, int *offset) { int len; - + memcpy(&residue->id, block->block_contents+*offset, sizeof(residue->id)); if(tng_data->input_endianness_swap_func_64) @@ -1905,7 +1905,7 @@ static tng_function_status tng_atom_data_read(tng_trajectory_t tng_data, int *offset) { int len; - + memcpy(&atom->id, block->block_contents+*offset, sizeof(atom->id)); if(tng_data->input_endianness_swap_func_64) @@ -2096,7 +2096,7 @@ static tng_function_status tng_molecules_block_read return(TNG_CRITICAL); } } - + /* Read each molecule from file */ for(i=0; i < tng_data->n_molecules; i++) { @@ -2115,7 +2115,7 @@ static tng_function_status tng_molecules_block_read } } offset += sizeof(molecule->id); - + // printf("Read id: %"PRId64" offset: %d\n", molecule->id, offset); len = tng_min(strlen(block->block_contents+offset) + 1, TNG_MAX_STR_LEN); molecule->name = malloc(len); @@ -2153,7 +2153,7 @@ static tng_function_status tng_molecules_block_read } offset += sizeof(int64_t); } - + memcpy(&molecule->n_chains, block->block_contents+offset, sizeof(molecule->n_chains)); @@ -2260,7 +2260,7 @@ static tng_function_status tng_molecules_block_read tng_chain_data_read(tng_data, block, chain, &offset); chain->residues = residue; - + /* Read the residues of the chain */ for(k=chain->n_residues; k--;) { @@ -2332,7 +2332,7 @@ static tng_function_status tng_molecules_block_read } } offset += sizeof(molecule->n_bonds); - + molecule->bonds = malloc(molecule->n_bonds * sizeof(struct tng_bond)); if(!molecule->bonds) @@ -2374,11 +2374,11 @@ static tng_function_status tng_molecules_block_read } } offset += sizeof(bond->to_atom_id); - + bond++; } } - + return(TNG_SUCCESS); } @@ -2428,7 +2428,7 @@ static tng_function_status tng_molecules_block_write for(j = molecule->n_chains; j--;) { len += sizeof(chain->id); - + if(!chain->name) { chain->name = malloc(1); @@ -2522,10 +2522,10 @@ static tng_function_status tng_molecules_block_write tng_block_destroy(&block); return(TNG_CRITICAL); } - + strcpy(block->name, "MOLECULES"); block->id = TNG_MOLECULES; - + block->block_contents_size = sizeof(tng_data->n_molecules) + (sizeof(molecule->id) + sizeof(molecule->quaternary_str) + @@ -2540,7 +2540,7 @@ static tng_function_status tng_molecules_block_write { block->block_contents_size += tng_data->n_molecules * sizeof(int64_t); } - + block->block_contents = malloc(block->block_contents_size); if(!block->block_contents) { @@ -2600,7 +2600,7 @@ static tng_function_status tng_molecules_block_write } } offset += sizeof(molecule->quaternary_str); - + if(!tng_data->var_num_atoms_flag) { memcpy(block->block_contents+offset, @@ -2700,7 +2700,7 @@ static tng_function_status tng_molecules_block_write atom++; } residue++; - } + } } else { @@ -2713,7 +2713,7 @@ static tng_function_status tng_molecules_block_write } } } - + memcpy(block->block_contents+offset, &molecule->n_bonds, sizeof(molecule->n_bonds)); if(tng_data->output_endianness_swap_func_64) @@ -2727,7 +2727,7 @@ static tng_function_status tng_molecules_block_write } } offset += sizeof(molecule->n_bonds); - + bond = molecule->bonds; for(j = molecule->n_bonds; j--;) { @@ -2744,7 +2744,7 @@ static tng_function_status tng_molecules_block_write } } offset += sizeof(bond->from_atom_id); - + memcpy(block->block_contents+offset, &bond->to_atom_id, sizeof(bond->to_atom_id)); if(tng_data->output_endianness_swap_func_64) @@ -2838,7 +2838,7 @@ static tng_function_status tng_frame_set_block_read file_pos = ftell(tng_data->input_file) - (block->block_contents_size + block->header_contents_size); - + if(hash_mode == TNG_USE_HASH) { hash_match_verify(block, &same_hash); @@ -2893,7 +2893,7 @@ static tng_function_status tng_frame_set_block_read } } offset += sizeof(frame_set->first_frame); - + memcpy(&frame_set->n_frames, block->block_contents + offset, sizeof(frame_set->n_frames)); if(tng_data->input_endianness_swap_func_64) @@ -2918,7 +2918,7 @@ static tng_function_status tng_frame_set_block_read { frame_set->molecule_cnt_list = malloc(sizeof(int64_t) * tng_data->n_molecules); - + if(!frame_set->molecule_cnt_list) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", @@ -2966,7 +2966,7 @@ static tng_function_status tng_frame_set_block_read } } offset += sizeof(frame_set->next_frame_set_file_pos); - + memcpy(&frame_set->prev_frame_set_file_pos, block->block_contents + offset, sizeof(frame_set->prev_frame_set_file_pos)); @@ -3041,7 +3041,7 @@ static tng_function_status tng_frame_set_block_read } } offset += sizeof(frame_set->long_stride_prev_frame_set_file_pos); - + return(TNG_SUCCESS); } @@ -3153,7 +3153,7 @@ static tng_function_status tng_frame_set_block_write } } - + memcpy(block->block_contents+offset, &frame_set->next_frame_set_file_pos, sizeof(frame_set->next_frame_set_file_pos)); if(tng_data->output_endianness_swap_func_64) @@ -3280,7 +3280,7 @@ static tng_function_status tng_trajectory_mapping_block_read tng_bool same_hash; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_particle_mapping_t mapping, mappings; if(tng_input_file_init(tng_data) != TNG_SUCCESS) @@ -3338,7 +3338,7 @@ static tng_function_status tng_trajectory_mapping_block_read } frame_set->mappings = mappings; mapping = &mappings[frame_set->n_mapping_blocks - 1]; - + memcpy(&mapping->num_first_particle, block->block_contents+offset, sizeof(mapping->num_first_particle)); @@ -3402,7 +3402,7 @@ static tng_function_status tng_trajectory_mapping_block_read memcpy(mapping->real_particle_numbers, block->block_contents + offset, mapping->n_particles * sizeof(int64_t)); } - + return(TNG_SUCCESS); } @@ -3539,7 +3539,7 @@ static tng_function_status tng_trajectory_mapping_block_write return(TNG_SUCCESS); } -/** Prepare a block for storing particle data +/** Prepare a block for storing particle data * @param tng_data is a trajectory data container. * @param block_type_flag specifies if this is a trajectory block or a * non-trajectory block. (TNG_TRAJECTORY_BLOCK or TNG_NON_TRAJECTORY_BLOCK) @@ -3552,9 +3552,9 @@ static tng_function_status tng_particle_data_block_create { tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_particle_data_t data; - + if(block_type_flag == TNG_TRAJECTORY_BLOCK) { frame_set->n_particle_data_blocks++; @@ -3751,7 +3751,7 @@ static tng_function_status tng_particle_data_read { block_type_flag = TNG_NON_TRAJECTORY_BLOCK; } - + block_index = -1; /* See if there is already a data block of this ID */ if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -3800,7 +3800,7 @@ static tng_function_status tng_particle_data_read n_particle_data_blocks - 1]; } data->block_id = block->id; - + data->block_name = malloc(strlen(block->name) + 1); if(!data->block_name) { @@ -3827,7 +3827,7 @@ static tng_function_status tng_particle_data_read { tot_n_particles = tng_data->n_particles; } - + /* Allocate memory */ if(!data->values || data->n_frames != n_frames || data->n_values_per_frame != n_values) @@ -3844,7 +3844,7 @@ static tng_function_status tng_particle_data_read } data->first_frame_with_data = first_frame_with_data; - + n_frames = tng_max(1, n_frames / stride_length); /* FIXME: If not using a union to store data a whole dimension @@ -3993,7 +3993,7 @@ static tng_function_status tng_particle_data_block_write union data_values **first_dim_values, *second_dim_values; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_particle_data_t data; tng_block_type block_type_flag; @@ -4062,7 +4062,7 @@ static tng_function_status tng_particle_data_block_write to be at least 1 */ n_frames = tng_max(1, data->n_frames); - + if(mapping && mapping->n_particles != 0) { n_particles = mapping->n_particles; @@ -4080,7 +4080,7 @@ static tng_function_status tng_particle_data_block_write n_particles = tng_data->n_particles; } } - + block->block_contents_size = sizeof(char) * 2 + sizeof(data->n_values_per_frame) + sizeof(data->codec_id) + @@ -4133,7 +4133,7 @@ static tng_function_status tng_particle_data_block_write { block->block_contents_size += sizeof(char); } - + if(block->block_contents) { free(block->block_contents); @@ -4246,7 +4246,7 @@ static tng_function_status tng_particle_data_block_write offset += sizeof(stride_length); } - + memcpy(block->block_contents+offset, &num_first_particle, sizeof(num_first_particle)); if(tng_data->output_endianness_swap_func_64) @@ -4274,7 +4274,7 @@ static tng_function_status tng_particle_data_block_write } offset += sizeof(n_particles); - + /* FIXME: If not using a union to store data a whole dimension or the * whole block can be written at once if byte swapping is not needed */ switch(data->datatype) @@ -4307,7 +4307,7 @@ static tng_function_status tng_particle_data_block_write } } break; - + case TNG_INT_DATA: for(i = 0; i < data->n_frames / stride_length; i++) { @@ -4416,9 +4416,9 @@ static tng_function_status tng_data_block_create { tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_non_particle_data_t data; - + if(block_type_flag == TNG_TRAJECTORY_BLOCK) { frame_set->n_data_blocks++; @@ -4595,7 +4595,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, default: size = sizeof(double); } - + block_index = -1; /* See if there is already a data block of this ID */ /* FIXME: Do not compare with block->id. Use ID as parameter instead. */ @@ -4623,7 +4623,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, } } } - + /* Otherwise create a data block */ if(block_index == -1) { @@ -4676,7 +4676,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, } data->first_frame_with_data = first_frame_with_data; - + n_frames = tng_max(1, n_frames / stride_length); /* FIXME: If not using a union to store data a whole dimension @@ -4794,7 +4794,7 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, char temp, dependency, *temp_name; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_non_particle_data_t data; tng_block_type block_type_flag; @@ -4863,7 +4863,7 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, to be at least 1 */ n_frames = tng_max(1, data->n_frames); - + block->block_contents_size = sizeof(char) * 2 + sizeof(data->n_values_per_frame) + sizeof(data->codec_id); @@ -4873,12 +4873,12 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, block->block_contents_size += sizeof(data->first_frame_with_data) + sizeof(data->stride_length); } - + if(data->codec_id != TNG_UNCOMPRESSED) { block->block_contents_size += sizeof(data->compression_multiplier); } - + if(data->datatype == TNG_CHAR_DATA) { for(i = n_frames; i--;) @@ -4902,7 +4902,7 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, else { dependency = 0; - } + } if(dependency & TNG_FRAME_DEPENDENT) { block->block_contents_size += sizeof(char); @@ -5176,8 +5176,8 @@ static tng_function_status tng_data_block_contents_read hash_match_verify(block, &same_hash); if(same_hash != TNG_TRUE) { - printf("Data block contents corrupt. Hashes do not match. %s: %d\n", - __FILE__, __LINE__); + printf("'%s' data block contents corrupt. Hashes do not match. %s: %d\n", + block->name, __FILE__, __LINE__); // return(TNG_FAILURE); } } @@ -5264,7 +5264,7 @@ static tng_function_status tng_data_block_contents_read } } offset += sizeof(first_frame_with_data); - + memcpy(&stride_length, block->block_contents+offset, sizeof(stride_length)); if(tng_data->input_endianness_swap_func_64) @@ -5292,7 +5292,7 @@ static tng_function_status tng_data_block_contents_read stride_length = 1; n_frames = 0; } - + if (dependency & TNG_PARTICLE_DEPENDENT) { memcpy(&num_first_particle, block->block_contents+offset, @@ -5364,7 +5364,7 @@ static tng_function_status tng_md5_hash_update(tng_trajectory_t tng_data, { free(block->block_contents); } - + block->block_contents = malloc(block->block_contents_size); fseek(tng_data->output_file, contents_start_pos, SEEK_SET); if(fread(block->block_contents, block->block_contents_size, 1, @@ -5406,7 +5406,7 @@ static tng_function_status tng_header_pointers_update } tng_data->input_file = tng_data->output_file; - + tng_block_init(&block); output_file_pos = ftell(tng_data->output_file); @@ -5429,7 +5429,7 @@ static tng_function_status tng_header_pointers_update tng_data->input_file = temp; pos = tng_data->first_trajectory_frame_set_output_file_pos; - + if(tng_data->input_endianness_swap_func_64) { if(tng_data->input_endianness_swap_func_64(tng_data, @@ -5440,15 +5440,15 @@ static tng_function_status tng_header_pointers_update __FILE__, __LINE__); } } - + if(fwrite(&pos, sizeof(int64_t), 1, tng_data->output_file) != 1) { tng_block_destroy(&block); return(TNG_CRITICAL); } - + pos = tng_data->last_trajectory_frame_set_output_file_pos; - + if(tng_data->input_endianness_swap_func_64) { if(tng_data->input_endianness_swap_func_64(tng_data, @@ -5473,7 +5473,7 @@ static tng_function_status tng_header_pointers_update } tng_block_destroy(&block); - + fseek(tng_data->output_file, output_file_pos, SEEK_SET); return(TNG_SUCCESS); @@ -5504,7 +5504,7 @@ static tng_function_status tng_frame_set_pointers_update tng_block_init(&block); output_file_pos = ftell(tng_data->output_file); - + tng_data->input_file = tng_data->output_file; frame_set = &tng_data->current_trajectory_frame_set; @@ -5517,7 +5517,7 @@ static tng_function_status tng_frame_set_pointers_update SEEK_SET); header_start_pos = frame_set->prev_frame_set_file_pos; - + if(tng_block_header_read(tng_data, block) != TNG_SUCCESS) { printf("Cannot read frame header. %s: %d\n", @@ -5557,7 +5557,7 @@ static tng_function_status tng_frame_set_pointers_update tng_md5_hash_update(tng_data, block, header_start_pos, contents_start_pos); } - + fseek(tng_data->output_file, output_file_pos, SEEK_SET); } @@ -5579,7 +5579,7 @@ static tng_function_status tng_frame_set_pointers_update } contents_start_pos = ftell(tng_data->output_file); - + fseek(tng_data->output_file, block->block_contents_size - 4 * sizeof(int64_t), SEEK_CUR); @@ -5602,7 +5602,7 @@ static tng_function_status tng_frame_set_pointers_update tng_block_destroy(&block); return(TNG_CRITICAL); } - + if(hash_mode == TNG_USE_HASH) { tng_md5_hash_update(tng_data, block, @@ -5660,9 +5660,9 @@ static tng_function_status tng_frame_set_pointers_update contents_start_pos); } } - + fseek(tng_data->output_file, output_file_pos, SEEK_SET); - + tng_data->input_file = temp; tng_block_destroy(&block); @@ -5682,7 +5682,7 @@ static tng_function_status tng_block_name_set(tng_trajectory_t tng_data, const char *new_name) { int len; - + len = tng_min(strlen(new_name) + 1, TNG_MAX_STR_LEN); /* If the currently stored string length is not enough to store the new @@ -5701,10 +5701,10 @@ static tng_function_status tng_block_name_set(tng_trajectory_t tng_data, __FILE__, __LINE__); return(TNG_CRITICAL); } - } - + } + strncpy(block->name, new_name, len); - + return(TNG_SUCCESS); } @@ -5778,7 +5778,7 @@ static tng_function_status tng_atom_init(tng_atom_t atom) { atom->name = 0; atom->atom_type = 0; - + return(TNG_SUCCESS); } @@ -5798,7 +5798,7 @@ static tng_function_status tng_atom_destroy(tng_atom_t atom) free(atom->atom_type); atom->atom_type = 0; } - + return(TNG_SUCCESS); } @@ -5810,7 +5810,7 @@ tng_function_status tng_molecule_add(tng_trajectory_t tng_data, int64_t *new_molecule_cnt_list; int id, i; tng_bool found_id = TNG_TRUE; - + new_molecules = realloc(tng_data->molecules, sizeof(struct tng_molecule) * (tng_data->n_molecules + 1)); @@ -5827,7 +5827,7 @@ tng_function_status tng_molecule_add(tng_trajectory_t tng_data, new_molecule_cnt_list = realloc(tng_data->molecule_cnt_list, sizeof(int64_t) * (tng_data->n_molecules + 1)); - + if(!new_molecule_cnt_list) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", @@ -5866,7 +5866,7 @@ tng_function_status tng_molecule_add(tng_trajectory_t tng_data, id++; } } - + (*molecule)->id = id; tng_data->n_molecules++; @@ -5962,9 +5962,9 @@ tng_function_status tng_molecule_chain_find(tng_trajectory_t tng_data, tng_chain_t *chain) { int i, n_chains; - + n_chains = molecule->n_chains; - + for(i = 0; i < n_chains; i++) { *chain = &molecule->chains[i]; @@ -5976,9 +5976,9 @@ tng_function_status tng_molecule_chain_find(tng_trajectory_t tng_data, } } } - + *chain = 0; - + return(TNG_FAILURE); } @@ -6016,7 +6016,7 @@ tng_function_status tng_molecule_chain_add(tng_trajectory_t tng_data, molecule->n_chains++; (*chain)->id = molecule->n_chains; - + return(TNG_SUCCESS); } @@ -6142,7 +6142,7 @@ tng_function_status tng_chain_residue_add(tng_trajectory_t tng_data, { chain->residues = *residue; } - + (*residue)->name = 0; tng_residue_name_set(tng_data, *residue, name); @@ -6154,7 +6154,7 @@ tng_function_status tng_chain_residue_add(tng_trajectory_t tng_data, molecule->n_residues++; (*residue)->id = chain->n_residues; - + return(TNG_SUCCESS); } @@ -6263,9 +6263,9 @@ tng_function_status tng_residue_atom_add(tng_trajectory_t tng_data, residue->n_atoms++; molecule->n_atoms++; - + (*atom)->id = molecule->n_atoms; - + return(TNG_SUCCESS); } @@ -6283,7 +6283,7 @@ tng_function_status tng_molecule_init(const tng_trajectory_t tng_data, molecule->atoms = 0; molecule->n_bonds = 0; molecule->bonds = 0; - + return(TNG_SUCCESS); } @@ -6297,7 +6297,7 @@ tng_function_status tng_molecule_destroy(const tng_trajectory_t tng_data, free(molecule->name); molecule->name = 0; } - + if(molecule->chains) { for(i = molecule->n_chains; i--;) @@ -6338,7 +6338,7 @@ tng_function_status tng_molecule_destroy(const tng_trajectory_t tng_data, molecule->atoms = 0; } molecule->n_atoms = 0; - + if(molecule->bonds) { free(molecule->bonds); @@ -6536,7 +6536,7 @@ tng_function_status tng_atom_name_of_particle_nr_get { return(TNG_FAILURE); } - + strncpy(name, atom->name, max_len - 1); name[max_len - 1] = 0; @@ -6662,7 +6662,7 @@ tng_function_status tng_particle_mapping_add mapping->num_first_particle = num_first_particle; mapping->n_particles = n_particles; - + mapping->real_particle_numbers = malloc(sizeof(int64_t) * n_particles); if(!mapping->real_particle_numbers) { @@ -6675,7 +6675,7 @@ tng_function_status tng_particle_mapping_add { mapping->real_particle_numbers[i] = mapping_table[i]; } - + return(TNG_SUCCESS); } @@ -6696,7 +6696,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) tng_data = *tng_data_p; frame_set = &tng_data->current_trajectory_frame_set; - + tng_data->input_file_path = 0; tng_data->input_file = 0; tng_data->input_file_len = 0; @@ -6712,7 +6712,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) tng_data->last_computer_name = 0; tng_data->last_pgp_signature = 0; tng_data->forcefield_name = 0; - + seconds = time(0); if ( seconds == -1) { @@ -6746,7 +6746,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) frame_set->n_mapping_blocks = 0; frame_set->mappings = 0; frame_set->molecule_cnt_list = 0; - + frame_set->n_particle_data_blocks = 0; frame_set->n_data_blocks = 0; @@ -6759,7 +6759,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) frame_set->medium_stride_prev_frame_set_file_pos = -1; frame_set->long_stride_next_frame_set_file_pos = -1; frame_set->long_stride_prev_frame_set_file_pos = -1; - + tng_data->n_molecules = 0; tng_data->molecules = 0; tng_data->molecule_cnt_list = 0; @@ -6779,7 +6779,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) tng_data->endianness_32 = TNG_LITTLE_ENDIAN_32; } - + /* 0x45670123 */ else if ( *(const uint8_t*)&endianness_32 == 0x45 ) { @@ -6792,7 +6792,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) { tng_data->endianness_64 = TNG_BIG_ENDIAN_64; } - + /* 0xEFCDAB8967452301 */ else if ( *(const uint8_t*)&endianness_64 == 0xEF ) { @@ -6810,7 +6810,7 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) { tng_data->endianness_64 = TNG_BYTE_PAIR_SWAP_64; } - + /* 0x23016745AB89EFCD */ else if ( *(const uint8_t*)&endianness_64 == 0x23 ) { @@ -6825,11 +6825,11 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) tng_data->input_endianness_swap_func_64 = 0; tng_data->output_endianness_swap_func_32 = 0; tng_data->output_endianness_swap_func_64 = 0; - + tng_data->current_trajectory_frame_set.next_frame_set_file_pos = -1; tng_data->current_trajectory_frame_set.prev_frame_set_file_pos = -1; tng_data->current_trajectory_frame_set.n_frames = 0; - + return(TNG_SUCCESS); } @@ -6847,31 +6847,31 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) { return(TNG_SUCCESS); } - + if(tng_data->input_file_path) { free(tng_data->input_file_path); tng_data->input_file_path = 0; } - + if(tng_data->input_file) { fclose(tng_data->input_file); tng_data->input_file = 0; } - + if(tng_data->output_file_path) { free(tng_data->output_file_path); tng_data->output_file_path = 0; } - + if(tng_data->output_file) { fclose(tng_data->output_file); tng_data->output_file = 0; } - + if(tng_data->first_program_name) { free(tng_data->first_program_name); @@ -6889,7 +6889,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(tng_data->first_user_name); tng_data->first_user_name = 0; } - + if(tng_data->last_user_name) { free(tng_data->last_user_name); @@ -6947,7 +6947,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(frame_set->molecule_cnt_list); frame_set->molecule_cnt_list = 0; } - + if(tng_data->var_num_atoms_flag) { n_particles = tng_data->current_trajectory_frame_set.n_particles; @@ -6969,7 +6969,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) 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); @@ -6979,7 +6979,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(tng_data->non_tr_particle_data); tng_data->non_tr_particle_data = 0; } - + if(tng_data->non_tr_data) { for(i = tng_data->n_data_blocks; i--;) @@ -6988,7 +6988,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) 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); @@ -6998,10 +6998,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(tng_data->non_tr_data); tng_data->non_tr_data = 0; } - + tng_data->n_particle_data_blocks = 0; tng_data->n_data_blocks = 0; - + if(frame_set->tr_particle_data) { for(i = frame_set->n_particle_data_blocks; i--; ) @@ -7018,7 +7018,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) 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); @@ -7028,7 +7028,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(frame_set->tr_particle_data); frame_set->tr_particle_data = 0; } - + if(frame_set->tr_data) { for(i = frame_set->n_data_blocks; i--;) @@ -7049,10 +7049,10 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(frame_set->tr_data); frame_set->tr_data = 0; } - + frame_set->n_particle_data_blocks = 0; frame_set->n_data_blocks = 0; - + if(tng_data->molecules) { for(i=tng_data->n_molecules; i--;) @@ -7071,7 +7071,7 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) free(*tng_data_p); *tng_data_p = 0; - + return(TNG_SUCCESS); } @@ -7102,7 +7102,7 @@ tng_function_status tng_trajectory_init_from_src(tng_trajectory_t src, { dest->input_file = 0; } - + dest->input_file_len = src->input_file_len; dest->output_file_path = 0; if(src->output_file) @@ -7205,13 +7205,13 @@ tng_function_status tng_input_file_set(tng_trajectory_t tng_data, { int len; char *temp; - + if(tng_data->input_file_path && strcmp(tng_data->input_file_path, file_name) == 0) { return(TNG_SUCCESS); } - + if(tng_data->input_file) { fclose(tng_data->input_file); @@ -7227,7 +7227,7 @@ tng_function_status tng_input_file_set(tng_trajectory_t tng_data, return(TNG_CRITICAL); } tng_data->input_file_path = temp; - + strncpy(tng_data->input_file_path, file_name, len); return(tng_input_file_init(tng_data)); @@ -7273,7 +7273,7 @@ tng_function_status tng_output_file_set(tng_trajectory_t tng_data, return(TNG_CRITICAL); } tng_data->output_file_path = temp; - + strncpy(tng_data->output_file_path, file_name, len); return(tng_output_file_init(tng_data)); @@ -7284,7 +7284,7 @@ tng_function_status tng_output_file_endianness_get { tng_endianness_32 end_32; tng_endianness_64 end_64; - + if(tng_data->output_endianness_swap_func_32) { /* If other endianness variants are added they must be added here as well */ @@ -7307,7 +7307,7 @@ tng_function_status tng_output_file_endianness_get { end_32 = tng_data->endianness_32; } - + if(tng_data->output_endianness_swap_func_64) { /* If other endianness variants are added they must be added here as well */ @@ -7349,7 +7349,7 @@ tng_function_status tng_output_file_endianness_get { return(TNG_FAILURE); } - + return(TNG_SUCCESS); } @@ -7867,7 +7867,7 @@ tng_function_status tng_num_molecules_get(const tng_trajectory_t tng_data, int64_t *n) { int64_t *cnt_list, cnt = 0, i; - + if(tng_data->var_num_atoms_flag == TNG_CONSTANT_N_ATOMS) { cnt_list = tng_data->molecule_cnt_list; @@ -7883,7 +7883,7 @@ tng_function_status tng_num_molecules_get(const tng_trajectory_t tng_data, } *n = cnt; - + return(TNG_SUCCESS); } @@ -7906,9 +7906,9 @@ tng_function_status tng_num_frame_sets_get(const tng_trajectory_t tng_data, tng_gen_block_t block; tng_function_status stat; int64_t cnt = 0; - + file_pos = tng_data->first_trajectory_frame_set_input_file_pos; - + tng_block_init(&block); fseek(tng_data->input_file, file_pos, @@ -7930,7 +7930,7 @@ tng_function_status tng_num_frame_sets_get(const tng_trajectory_t tng_data, } ++cnt; - + file_pos = tng_data->current_trajectory_frame_set_input_file_pos; long_stride_length = tng_data->long_stride_length; @@ -8021,7 +8021,7 @@ tng_function_status tng_num_frame_sets_get(const tng_trajectory_t tng_data, } tng_block_destroy(&block); - + *n = tng_data->n_trajectory_frame_sets = cnt; return(TNG_SUCCESS); @@ -8047,7 +8047,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, tng_function_status stat; stat = tng_num_frame_sets_get(tng_data, &n_frame_sets); - + if(nr >= n_frame_sets) { return(TNG_FAILURE); @@ -8165,12 +8165,12 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + /* Take one step forward until the right frame set is found */ while(file_pos > 0 && curr_nr < nr) { file_pos = frame_set->next_frame_set_file_pos; - + if(file_pos > 0) { ++curr_nr; @@ -8198,7 +8198,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + /* Take long steps backward until a long step backward would be too long * or the right frame set is found */ while(file_pos > 0 && curr_nr - long_stride_length >= nr) @@ -8231,7 +8231,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + /* Take medium steps backward until a medium step backward would be too long * or the right frame set is found */ while(file_pos > 0 && curr_nr - medium_stride_length >= nr) @@ -8264,7 +8264,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + /* Take one step backward until the right frame set is found */ while(file_pos > 0 && curr_nr > nr) { @@ -8296,7 +8296,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + /* If for some reason the current frame set is not yet found, * take one step forward until the right frame set is found */ while(file_pos > 0 && curr_nr < nr) @@ -8329,7 +8329,7 @@ tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, } } } - + tng_block_destroy(&block); return(TNG_FAILURE); } @@ -8405,10 +8405,10 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, } } } - + first_frame = tng_max(frame_set->first_frame, 0); last_frame = first_frame + frame_set->n_frames - 1; - + if(frame >= first_frame && frame <= last_frame) { tng_block_destroy(&block); @@ -8449,7 +8449,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* Take medium steps forward until a medium step forward would be too long * or the right frame set is found */ while(file_pos > 0 && first_frame + medium_stride_length * @@ -8484,7 +8484,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* Take one step forward until the right frame set is found */ while(file_pos > 0 && first_frame < frame && last_frame < frame) { @@ -8517,7 +8517,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* Take long steps backward until a long step backward would be too long * or the right frame set is found */ while(file_pos > 0 && first_frame - long_stride_length * @@ -8552,7 +8552,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* Take medium steps backward until a medium step backward would be too long * or the right frame set is found */ while(file_pos > 0 && first_frame - medium_stride_length * @@ -8587,7 +8587,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* Take one step backward until the right frame set is found */ while(file_pos > 0 && first_frame > frame && last_frame > frame) { @@ -8620,7 +8620,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + /* If for some reason the current frame set is not yet found, * take one step forward until the right frame set is found */ while(file_pos > 0 && first_frame < frame && last_frame < frame) @@ -8654,7 +8654,7 @@ tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } - + tng_block_destroy(&block); return(TNG_FAILURE); } @@ -8770,7 +8770,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, tng_gen_block_t block; tng_data->n_trajectory_frame_sets = 0; - + if(tng_input_file_init(tng_data) != TNG_SUCCESS) { return(TNG_CRITICAL); @@ -8782,7 +8782,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, tng_data->input_file_len = ftell(tng_data->input_file); fseek(tng_data->input_file, 0, SEEK_SET); } - + tng_block_init(&block); /* Non trajectory blocks (they come before the trajectory * blocks in the file) */ @@ -8806,7 +8806,7 @@ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, } tng_block_destroy(&block); - + return(TNG_SUCCESS); } @@ -8829,7 +8829,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, tng_data->input_file_path, __FILE__, __LINE__); return(TNG_CRITICAL); } - + if(tng_molecules_block_write(tng_data, hash_mode) != TNG_SUCCESS) { @@ -8856,7 +8856,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, } tng_block_destroy(&data_block); - + return(TNG_SUCCESS); } @@ -8907,7 +8907,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, { file_pos = tng_data->first_trajectory_frame_set_input_file_pos; } - + if(file_pos > 0) { fseek(tng_data->input_file, @@ -8918,7 +8918,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, { return(TNG_FAILURE); } - + tng_block_init(&block); if(!tng_data->input_file_len) @@ -8937,7 +8937,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, } tng_data->current_trajectory_frame_set_input_file_pos = file_pos; - + if(tng_block_read_next(tng_data, block, hash_mode) == TNG_SUCCESS) { @@ -8973,7 +8973,7 @@ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, } tng_block_destroy(&block); - + return(TNG_SUCCESS); } @@ -8984,11 +8984,11 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, tng_gen_block_t block; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; - + tng_function_status stat; tng_data->current_trajectory_frame_set_output_file_pos = - tng_data->last_trajectory_frame_set_output_file_pos = + tng_data->last_trajectory_frame_set_output_file_pos = ftell(tng_data->output_file); if(tng_data->current_trajectory_frame_set_output_file_pos <= 0) @@ -9048,14 +9048,14 @@ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, /* Update pointers in the general info block */ stat = tng_header_pointers_update(tng_data, hash_mode); - + if(stat == TNG_SUCCESS) { stat = tng_frame_set_pointers_update(tng_data, hash_mode); } tng_block_destroy(&block); - + return(stat); } @@ -9081,7 +9081,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, frame_set->prev_frame_set_file_pos = tng_data->current_trajectory_frame_set_output_file_pos; } - + tng_data->current_trajectory_frame_set_output_file_pos = ftell(tng_data->output_file); @@ -9119,12 +9119,12 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, { tng_block_init(&block); tng_data->input_file = tng_data->output_file; - + curr_pos = ftell(tng_data->output_file); fseek(tng_data->output_file, frame_set->medium_stride_prev_frame_set_file_pos, SEEK_SET); - + if(tng_block_header_read(tng_data, block) != TNG_SUCCESS) { printf("Cannot read frame header. %s: %d\n", @@ -9158,9 +9158,9 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, __FILE__, __LINE__); } } - + tng_block_destroy(&block); - + /* Set the long range pointers */ if(tng_data->n_trajectory_frame_sets == tng_data->long_stride_length + 1) { @@ -9196,7 +9196,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, sizeof(int64_t), SEEK_CUR); tng_block_destroy(&block); - + if(fread(&frame_set->long_stride_prev_frame_set_file_pos, sizeof(frame_set->long_stride_prev_frame_set_file_pos), 1, tng_data->output_file) == 0) @@ -9219,7 +9219,7 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, } } - + tng_data->input_file = temp; fseek(tng_data->output_file, curr_pos, SEEK_SET); } @@ -9447,7 +9447,7 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, } } } - + return(TNG_SUCCESS); } @@ -9470,9 +9470,9 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, tng_trajectory_frame_set_t frame_set; tng_particle_data_t data; void *orig; - + frame_set = &tng_data->current_trajectory_frame_set; - + block_index = -1; /* See if there is already a data block of this ID */ if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -9678,8 +9678,8 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, } } } - - + + return(TNG_SUCCESS); } @@ -9717,13 +9717,13 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, tng_data->last_trajectory_frame_set_output_file_pos; tng_data->current_trajectory_frame_set_input_file_pos = tng_data->current_trajectory_frame_set_output_file_pos; - + tng_data->input_file = tng_data->output_file; stat = tng_frame_set_of_frame_find(tng_data, frame_nr); frame_set = &tng_data->current_trajectory_frame_set; - + if(stat != TNG_SUCCESS) { last_frame = tng_data->current_trajectory_frame_set.first_frame + @@ -9756,13 +9756,13 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, } tng_block_init(&block); - + file_pos = tng_data->current_trajectory_frame_set_output_file_pos; - + fseek(tng_data->output_file, 0, SEEK_END); output_file_len = ftell(tng_data->output_file); fseek(tng_data->output_file, file_pos, SEEK_SET); - + /* Read past the frame set block first */ stat = tng_block_header_read(tng_data, block); if(stat == TNG_CRITICAL) @@ -9841,14 +9841,14 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - + if(fread(&data.n_values_per_frame, sizeof(data.n_values_per_frame), 1, tng_data->input_file) == 0) { printf("Error reading file. %s: %d\n", __FILE__, __LINE__); tng_block_destroy(&block); return(TNG_CRITICAL); - } + } if(tng_data->output_endianness_swap_func_64) { if(tng_data->output_endianness_swap_func_64(tng_data, @@ -10037,7 +10037,7 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, } fflush(tng_data->output_file); - + /* If the last frame has been written update the hash */ if(hash_mode == TNG_USE_HASH && (frame_nr + data.stride_length - data.first_frame_with_data) >= @@ -10048,7 +10048,7 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, } tng_block_destroy(&block); - + return(TNG_SUCCESS); } @@ -10073,7 +10073,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_particle_mapping_t mapping; char dependency, sparse_data, datatype; void *copy; - + if(tng_output_file_init(tng_data) != TNG_SUCCESS) { printf("Cannot initialise destination file. %s: %d\n", @@ -10094,7 +10094,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_data->input_file = tng_data->output_file; stat = tng_frame_set_of_frame_find(tng_data, frame_nr); - + frame_set = &tng_data->current_trajectory_frame_set; if(stat != TNG_SUCCESS) @@ -10120,7 +10120,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, /* Read mapping blocks from the last frame set */ tng_block_init(&block); - + stat = tng_block_header_read(tng_data, block); while(file_pos < output_file_len && stat != TNG_CRITICAL && @@ -10163,7 +10163,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_block_init(&block); - + file_pos = tng_data->current_trajectory_frame_set_output_file_pos; fseek(tng_data->output_file, 0, SEEK_END); @@ -10184,7 +10184,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, } fseek(tng_data->output_file, block->block_contents_size, SEEK_CUR); - + if(tng_data->var_num_atoms_flag) { tot_n_particles = frame_set->n_particles; @@ -10193,7 +10193,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, { tot_n_particles = tng_data->n_particles; } - + if(val_n_particles < tot_n_particles) { mapping_block_end_pos = -1; @@ -10252,7 +10252,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, } fseek(tng_data->output_file, mapping_block_end_pos, SEEK_SET); } - + /* Read all block headers until next frame set block or * until the wanted block id is found */ stat = tng_block_header_read(tng_data, block); @@ -10282,7 +10282,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, contents_size = block->block_contents_size; header_size = block->header_contents_size; - + header_pos = ftell(tng_data->output_file) - header_size; frame_set = &tng_data->current_trajectory_frame_set; @@ -10292,9 +10292,9 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - + data.datatype = datatype; - + if(fread(&dependency, sizeof(dependency), 1, tng_data->input_file) == 0) { printf("Error reading file. %s: %d\n", __FILE__, __LINE__); @@ -10313,14 +10313,14 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_data->current_trajectory_frame_set_input_file_pos = temp_current; return(TNG_FAILURE); } - + if(fread(&sparse_data, sizeof(sparse_data), 1, tng_data->input_file) == 0) { printf("Error reading file. %s: %d\n", __FILE__, __LINE__); tng_block_destroy(&block); return(TNG_CRITICAL); - } - + } + if(fread(&data.n_values_per_frame, sizeof(data.n_values_per_frame), 1, tng_data->input_file) == 0) { @@ -10345,7 +10345,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, printf("Error reading file. %s: %d\n", __FILE__, __LINE__); tng_block_destroy(&block); return(TNG_CRITICAL); - } + } if(tng_data->output_endianness_swap_func_64) { if(tng_data->output_endianness_swap_func_64(tng_data, @@ -10356,7 +10356,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, __FILE__, __LINE__); } } - + if(data.codec_id != TNG_UNCOMPRESSED) { if(fread(&data.compression_multiplier, @@ -10367,7 +10367,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_CRITICAL); } - + if(tng_data->output_endianness_swap_func_64) { if(tng_data->output_endianness_swap_func_64(tng_data, @@ -10466,14 +10466,14 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, } } - + tng_data->input_file = temp; tng_data->first_trajectory_frame_set_input_file_pos = temp_first; tng_data->last_trajectory_frame_set_input_file_pos = temp_last; tng_data->current_trajectory_frame_set_input_file_pos = temp_current; - + switch(data.datatype) { case(TNG_INT_DATA): @@ -10506,7 +10506,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_block_destroy(&block); return(TNG_FAILURE); } - + fseek(tng_data->output_file, file_pos, SEEK_CUR); /* If the endianness is not big endian the data needs to be swapped */ @@ -10565,7 +10565,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_md5_hash_update(tng_data, block, header_pos, header_pos + header_size); } - + tng_block_destroy(&block); return(TNG_SUCCESS); } @@ -10577,7 +10577,7 @@ tng_function_status tng_data_values_free(const tng_trajectory_t tng_data, const tng_data_type type) { int i, j; - + if(values) { for(i = 0; i < n_frames; i++) @@ -10719,7 +10719,7 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, { return(stat); } - + for(i = frame_set->n_data_blocks; i-- ;) { data = &frame_set->tr_data[i]; @@ -10798,7 +10798,7 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, } free(new_data); - + return(TNG_SUCCESS); } @@ -11115,10 +11115,10 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, *n_frames = tng_max(1, data->n_frames); *values = new_data->values; - + free(new_data); } - + *type = data->datatype; /* It's not very elegant to reuse so much of the code in the different case * statements, but it's unnecessarily slow to have the switch-case block @@ -11180,7 +11180,7 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, } } } - + return(TNG_SUCCESS); } @@ -11211,7 +11211,7 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, return(stat); } - + tng_block_init(&block); file_pos = ftell(tng_data->input_file); /* Read all blocks until next frame set block */ @@ -11236,7 +11236,7 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, { return(stat); } - + frame_set = &tng_data->current_trajectory_frame_set; /* See if there is already a data block of this ID. @@ -11283,7 +11283,7 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, new_data->datatype = data->datatype; *n_values_per_frame = data->n_values_per_frame; if(tng_allocate_particle_data_mem(tng_data, new_data, n_frames, - data->stride_length, + data->stride_length, *n_particles, data->n_values_per_frame) != TNG_SUCCESS) { @@ -11835,7 +11835,7 @@ tng_function_status tng_molecule_chain_find_(tng_trajectory_t tng_data, { char *n = malloc(name_len + 1); tng_function_status stat; - + strncpy(n, name, name_len); n[name_len] = 0; stat = tng_molecule_chain_find(tng_data, molecule, n, id, chain); |