diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/trg_io.c | 344 | ||||
| -rw-r--r-- | src/lib/trg_io.h | 152 | ||||
| -rw-r--r-- | src/tests/trg_io_testing.c | 2 |
3 files changed, 249 insertions, 249 deletions
diff --git a/src/lib/trg_io.c b/src/lib/trg_io.c index c05d078..bc4424d 100644 --- a/src/lib/trg_io.c +++ b/src/lib/trg_io.c @@ -37,7 +37,7 @@ /* This function swaps the byte order of a 32 bit numerical variable. It does not only work with integer, but e.g. floats need casting */ static inline trg_function_status trg_swap_byte_order_32 - (const struct trg_trajectory *trg_data, uint32_t *v) + (const struct trg_trajectory *trg_data, int32_t *v) { switch(trg_data->endianness_32) { @@ -68,7 +68,7 @@ static inline trg_function_status trg_swap_byte_order_32 The byte order swapping routine can convert five different byte orders to big endian. */ static inline trg_function_status trg_swap_byte_order_64 - (const struct trg_trajectory *trg_data, uint64_t *v) + (const struct trg_trajectory *trg_data, int64_t *v) { switch(trg_data->endianness_64) { @@ -444,7 +444,7 @@ static trg_function_status trg_write_block_header if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->header_contents)) + (int64_t *)(block->header_contents)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -458,7 +458,7 @@ static trg_function_status trg_write_block_header if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->header_contents+offset)) + (int64_t *)(block->header_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -471,7 +471,7 @@ static trg_function_status trg_write_block_header if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->header_contents+offset)) + (int64_t *)(block->header_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -491,7 +491,7 @@ static trg_function_status trg_write_block_header if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->header_contents+offset)) + (int64_t *)(block->header_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -846,7 +846,7 @@ static trg_function_status trg_write_general_info_block sizeof(trg_data->time)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -872,7 +872,7 @@ static trg_function_status trg_write_general_info_block sizeof(trg_data->frame_set_n_frames)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -887,7 +887,7 @@ static trg_function_status trg_write_general_info_block sizeof(trg_data->first_trajectory_frame_set_input_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -902,7 +902,7 @@ static trg_function_status trg_write_general_info_block sizeof(trg_data->last_trajectory_frame_set_input_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -917,7 +917,7 @@ static trg_function_status trg_write_general_info_block sizeof(trg_data->stride_length)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -1041,7 +1041,7 @@ static trg_function_status trg_read_molecules_block { free(trg_data->molecule_cnt_list); } - trg_data->molecule_cnt_list = (uint64_t *) malloc(sizeof(uint64_t) * + trg_data->molecule_cnt_list = (int64_t *) malloc(sizeof(int64_t) * trg_data->n_molecules); if(!trg_data->molecule_cnt_list) { @@ -1092,7 +1092,7 @@ static trg_function_status trg_read_molecules_block { memcpy(&trg_data->molecule_cnt_list[i], block->block_contents+offset, - sizeof(uint64_t)); + sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, @@ -1102,7 +1102,7 @@ static trg_function_status trg_read_molecules_block __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); } @@ -1534,7 +1534,7 @@ static trg_function_status trg_write_molecules_block if(!trg_data->var_num_atoms_flag) { - block->block_contents_size += trg_data->n_molecules * sizeof(uint64_t); + block->block_contents_size += trg_data->n_molecules * sizeof(int64_t); } if(block->block_contents) @@ -1555,7 +1555,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1573,7 +1573,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1592,7 +1592,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1604,18 +1604,18 @@ static trg_function_status trg_write_molecules_block if(!trg_data->var_num_atoms_flag) { memcpy(block->block_contents+offset, - &trg_data->molecule_cnt_list[i], sizeof(uint64_t)); + &trg_data->molecule_cnt_list[i], sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); } memcpy(block->block_contents+offset, &molecule->n_chains, @@ -1623,7 +1623,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1637,7 +1637,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1651,7 +1651,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1667,7 +1667,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1685,7 +1685,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1701,7 +1701,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1719,7 +1719,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1736,7 +1736,7 @@ static trg_function_status trg_write_molecules_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1764,7 +1764,7 @@ static trg_function_status trg_write_molecules_block sizeof(molecule->n_bonds)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -1781,7 +1781,7 @@ static trg_function_status trg_write_molecules_block sizeof(bond->from_atom_id)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -1795,7 +1795,7 @@ static trg_function_status trg_write_molecules_block sizeof(bond->to_atom_id)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -1834,7 +1834,7 @@ static trg_function_status trg_read_frame_set_block struct trg_gen_block *block) { int i, file_pos, offset = 0; - uint64_t prev_n_particles; + int64_t prev_n_particles; trg_bool same_hash; struct trg_trajectory_frame_set *frame_set = &trg_data->current_trajectory_frame_set; @@ -1949,12 +1949,12 @@ static trg_function_status trg_read_frame_set_block if(!frame_set->molecule_cnt_list) { frame_set->molecule_cnt_list = - (uint64_t *) malloc(sizeof(uint64_t) * trg_data->n_molecules); + (int64_t *) malloc(sizeof(int64_t) * trg_data->n_molecules); if(!frame_set->molecule_cnt_list) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - sizeof(uint64_t) * trg_data->n_molecules, + sizeof(int64_t) * trg_data->n_molecules, __FILE__, __LINE__); trg_destroy_block(block); return(TRG_CRITICAL); @@ -1964,7 +1964,7 @@ static trg_function_status trg_read_frame_set_block { memcpy(&frame_set->molecule_cnt_list[i], block->block_contents + offset, - sizeof(uint64_t)); + sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, @@ -1975,7 +1975,7 @@ static trg_function_status trg_read_frame_set_block __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); frame_set->n_particles += trg_data->molecules[i].n_atoms * frame_set->molecule_cnt_list[i]; } @@ -2065,7 +2065,7 @@ static trg_function_status trg_write_frame_set_block write_mode mode) { char *temp_name; - uint64_t i; + int64_t i; int offset = 0, name_len; struct trg_trajectory_frame_set *frame_set = &trg_data->current_trajectory_frame_set; @@ -2120,10 +2120,10 @@ static trg_function_status trg_write_frame_set_block } strcpy(block->name, "TRAJECTORY FRAME SET"); - block->block_contents_size = sizeof(uint64_t) * 6; + block->block_contents_size = sizeof(int64_t) * 6; if(trg_data->var_num_atoms_flag) { - block->block_contents_size += sizeof(uint64_t) * trg_data->n_molecules; + block->block_contents_size += sizeof(int64_t) * trg_data->n_molecules; } if(block->block_contents) @@ -2143,7 +2143,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->first_frame)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents)) != TRG_SUCCESS) { @@ -2157,7 +2157,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->n_frames)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2173,10 +2173,10 @@ static trg_function_status trg_write_frame_set_block { memcpy(block->block_contents+offset, &frame_set->molecule_cnt_list[i], - sizeof(uint64_t)); + sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2184,7 +2184,7 @@ static trg_function_status trg_write_frame_set_block __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); } } @@ -2193,7 +2193,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->next_frame_set_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2207,7 +2207,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->prev_frame_set_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2222,7 +2222,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->long_stride_next_frame_set_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2237,7 +2237,7 @@ static trg_function_status trg_write_frame_set_block sizeof(frame_set->long_stride_prev_frame_set_file_pos)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2270,7 +2270,7 @@ static trg_function_status trg_read_trajectory_toc_block (struct trg_trajectory *trg_data, struct trg_gen_block *block) { - uint64_t i, old_n_blocks; + int64_t i, old_n_blocks; int offset = 0, len; trg_bool same_hash; struct trg_frame_set_toc *toc = @@ -2354,7 +2354,7 @@ static trg_function_status trg_read_trajectory_toc_block if(!toc->block_names) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - toc->n_blocks * sizeof(uint64_t), __FILE__, __LINE__); + toc->n_blocks * sizeof(int64_t), __FILE__, __LINE__); trg_destroy_block(block); return(TRG_CRITICAL); } @@ -2386,7 +2386,7 @@ static trg_function_status trg_write_trajectory_toc_block write_mode mode) { char *temp_name; - uint64_t i; + int64_t i; int offset = 0, name_len; struct trg_frame_set_toc *toc = &trg_data->current_trajectory_frame_set.contents; @@ -2441,7 +2441,7 @@ static trg_function_status trg_write_trajectory_toc_block } strcpy(block->name, "BLOCK TABLE OF CONTENTS"); - block->block_contents_size = sizeof(uint64_t); + block->block_contents_size = sizeof(int64_t); for(i = toc->n_blocks; i--;) { @@ -2464,7 +2464,7 @@ static trg_function_status trg_write_trajectory_toc_block memcpy(block->block_contents, &toc->n_blocks, sizeof(toc->n_blocks)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents)) != TRG_SUCCESS) { @@ -2506,7 +2506,7 @@ static trg_function_status trg_read_trajectory_mapping_block (struct trg_trajectory *trg_data, struct trg_gen_block *block) { - uint64_t i, old_n_particles; + int64_t i, old_n_particles; int offset = 0; trg_bool same_hash; struct trg_trajectory_frame_set *frame_set = @@ -2611,11 +2611,11 @@ static trg_function_status trg_read_trajectory_mapping_block free(mapping->real_particle_numbers); } mapping->real_particle_numbers = malloc(mapping->n_particles * - sizeof(uint64_t)); + sizeof(int64_t)); if(!mapping->real_particle_numbers) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - mapping->n_particles * sizeof(uint64_t), __FILE__, __LINE__); + mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__); trg_destroy_block(block); return(TRG_CRITICAL); } @@ -2625,7 +2625,7 @@ static trg_function_status trg_read_trajectory_mapping_block { memcpy(&mapping->real_particle_numbers[i], block->block_contents + offset, - sizeof(uint64_t)); + sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, @@ -2636,7 +2636,7 @@ static trg_function_status trg_read_trajectory_mapping_block __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); } return(TRG_SUCCESS); @@ -2712,7 +2712,7 @@ static trg_function_status trg_write_trajectory_mapping_block } strcpy(block->name, "PARTICLE MAPPING"); - block->block_contents_size = sizeof(uint64_t) * (2 + mapping->n_particles); + block->block_contents_size = sizeof(int64_t) * (2 + mapping->n_particles); if(block->block_contents) { @@ -2731,7 +2731,7 @@ static trg_function_status trg_write_trajectory_mapping_block sizeof(mapping->num_first_particle)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents)) != TRG_SUCCESS) { @@ -2745,7 +2745,7 @@ static trg_function_status trg_write_trajectory_mapping_block sizeof(mapping->n_particles)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2758,10 +2758,10 @@ static trg_function_status trg_write_trajectory_mapping_block for(i = 0; i < mapping->n_particles; i++) { memcpy(block->block_contents+offset, &mapping->real_particle_numbers[i], - sizeof(uint64_t)); + sizeof(int64_t)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -2769,7 +2769,7 @@ static trg_function_status trg_write_trajectory_mapping_block __FILE__, __LINE__); } } - offset += sizeof(uint64_t); + offset += sizeof(int64_t); } @@ -2844,12 +2844,12 @@ static trg_function_status trg_create_particle_data_block trg_function_status trg_allocate_particle_data_mem (struct trg_trajectory *trg_data, struct trg_particle_data *data, - uint64_t n_frames, - const uint64_t n_particles, - const uint64_t n_values_per_frame) + int64_t n_frames, + const int64_t n_particles, + const int64_t n_values_per_frame) { union data_values ***values; - uint64_t i, j, k; + int64_t i, j, k; for(i = data->n_frames; i--;) { @@ -2915,16 +2915,16 @@ static trg_function_status trg_read_particle_data struct trg_gen_block *block, int *offset, const char datatype, - const uint64_t first_particle_number, - const uint64_t n_particles, - const uint64_t first_frame_with_data, - const uint64_t stride_length, - uint64_t n_frames, - const uint64_t n_values, - const uint64_t codec_id, - const uint64_t multiplier) + const int64_t first_particle_number, + const int64_t n_particles, + const int64_t first_frame_with_data, + const int64_t stride_length, + int64_t n_frames, + const int64_t n_values, + const int64_t codec_id, + const int64_t multiplier) { - uint64_t block_index, i, j, k, tot_n_particles; + int64_t block_index, i, j, k, tot_n_particles; int size, len; struct trg_particle_data *data; struct trg_trajectory_frame_set *frame_set = @@ -2937,7 +2937,7 @@ static trg_function_status trg_read_particle_data size = 1; break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_FLOAT_DATA: size = sizeof(float); @@ -3067,7 +3067,7 @@ static trg_function_status trg_read_particle_data if(trg_data->endianness_32 != TRG_BIG_ENDIAN_32) { if(trg_swap_byte_order_32(trg_data, - (uint32_t *) &data->values[i][j][k]) != TRG_SUCCESS) + (int32_t *) &data->values[i][j][k]) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3083,7 +3083,7 @@ static trg_function_status trg_read_particle_data if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *) &data->values[i][j][k].i) != TRG_SUCCESS) + (int64_t *) &data->values[i][j][k].i) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3118,7 +3118,7 @@ static trg_function_status trg_read_particle_data if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *) &data->values[i][j][k].d) != TRG_SUCCESS) + (int64_t *) &data->values[i][j][k].d) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3141,7 +3141,7 @@ static trg_function_status trg_write_particle_data_block const struct trg_particle_mapping *mapping, const write_mode mode) { - uint64_t n_particles, num_first_particle, n_frames; + int64_t n_particles, num_first_particle, n_frames; int i, j, k, offset = 0, size, len; char temp, *temp_name; struct trg_trajectory_frame_set *frame_set = @@ -3170,7 +3170,7 @@ static trg_function_status trg_write_particle_data_block size = 1; break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_FLOAT_DATA: size = sizeof(float); @@ -3322,7 +3322,7 @@ static trg_function_status trg_write_particle_data_block sizeof(data->n_values_per_frame)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -3336,7 +3336,7 @@ static trg_function_status trg_write_particle_data_block sizeof(data->codec_id)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -3352,7 +3352,7 @@ static trg_function_status trg_write_particle_data_block sizeof(data->compression_multiplier)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -3369,7 +3369,7 @@ static trg_function_status trg_write_particle_data_block sizeof(data->first_frame_with_data)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -3383,7 +3383,7 @@ static trg_function_status trg_write_particle_data_block sizeof(data->stride_length)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -3399,7 +3399,7 @@ static trg_function_status trg_write_particle_data_block sizeof(num_first_particle)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -3412,7 +3412,7 @@ static trg_function_status trg_write_particle_data_block memcpy(block->block_contents+offset, &n_particles, sizeof(n_particles)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents+offset)) != TRG_SUCCESS) { @@ -3458,7 +3458,7 @@ static trg_function_status trg_write_particle_data_block if(trg_data->endianness_32 != TRG_BIG_ENDIAN_32) { if(trg_swap_byte_order_32(trg_data, - (uint32_t *)(block->block_contents+offset)) + (int32_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " @@ -3474,7 +3474,7 @@ static trg_function_status trg_write_particle_data_block if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " @@ -3557,11 +3557,11 @@ static trg_function_status trg_create_data_block trg_function_status trg_allocate_data_mem (struct trg_trajectory *trg_data, struct trg_data *data, - uint64_t n_frames, - const uint64_t n_values_per_frame) + int64_t n_frames, + const int64_t n_values_per_frame) { union data_values **values; - uint64_t i, j; + int64_t i, j; for(i = data->n_frames; i--;) { @@ -3620,14 +3620,14 @@ static trg_function_status trg_read_data(struct trg_trajectory *trg_data, struct trg_gen_block *block, int *offset, const char datatype, - const uint64_t first_frame_with_data, - const uint64_t stride_length, - uint64_t n_frames, - const uint64_t n_values, - const uint64_t codec_id, - const uint64_t multiplier) + const int64_t first_frame_with_data, + const int64_t stride_length, + int64_t n_frames, + const int64_t n_values, + const int64_t codec_id, + const int64_t multiplier) { - uint64_t block_index, i, j; + int64_t block_index, i, j; int size, len; struct trg_data *data; struct trg_trajectory_frame_set *frame_set = @@ -3651,7 +3651,7 @@ static trg_function_status trg_read_data(struct trg_trajectory *trg_data, size = 1; break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_FLOAT_DATA: size = sizeof(float); @@ -3774,7 +3774,7 @@ static trg_function_status trg_read_data(struct trg_trajectory *trg_data, if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *) &data->values[i][j].i) != TRG_SUCCESS) + (int64_t *) &data->values[i][j].i) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3789,7 +3789,7 @@ static trg_function_status trg_read_data(struct trg_trajectory *trg_data, if(trg_data->endianness_32 != TRG_BIG_ENDIAN_32) { if(trg_swap_byte_order_32(trg_data, - (uint32_t *) &data->values[i][j]) != TRG_SUCCESS) + (int32_t *) &data->values[i][j]) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3805,7 +3805,7 @@ static trg_function_status trg_read_data(struct trg_trajectory *trg_data, if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *) &data->values[i][j].d) != TRG_SUCCESS) + (int64_t *) &data->values[i][j].d) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " "%s: %d\n", @@ -3824,7 +3824,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, const int block_index, const write_mode mode) { - uint64_t n_frames; + int64_t n_frames; int i, j, offset = 0, size, len; char temp, *temp_name; struct trg_trajectory_frame_set *frame_set = @@ -3863,7 +3863,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, size = 1; break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_FLOAT_DATA: size = sizeof(float); @@ -3999,7 +3999,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, sizeof(data->n_values_per_frame)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -4014,7 +4014,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, sizeof(data->codec_id)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -4031,7 +4031,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, sizeof(data->compression_multiplier)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -4049,7 +4049,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, sizeof(data->first_frame_with_data)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -4064,7 +4064,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, sizeof(data->stride_length)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *) + if(trg_swap_byte_order_64(trg_data, (int64_t *) (block->block_contents + offset)) != TRG_SUCCESS) { @@ -4106,7 +4106,7 @@ static trg_function_status trg_write_data_block(struct trg_trajectory *trg_data, if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { if(trg_swap_byte_order_64(trg_data, - (uint64_t *)(block->block_contents+offset)) + (int64_t *)(block->block_contents+offset)) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. " @@ -4143,8 +4143,8 @@ static trg_function_status trg_read_data_block_contents (struct trg_trajectory *trg_data, struct trg_gen_block *block) { - uint64_t n_values, codec_id, n_frames, first_frame_with_data; - uint64_t steps_between_data, block_n_particles, first_particle_number; + int64_t n_values, codec_id, n_frames, first_frame_with_data; + int64_t steps_between_data, block_n_particles, first_particle_number; double multiplier; char datatype, dependency, sparse_data; int offset = 0; @@ -4253,7 +4253,7 @@ static trg_function_status trg_read_data_block_contents sizeof(multiplier)); if(trg_data->endianness_64 != TRG_BIG_ENDIAN_64) { - if(trg_swap_byte_order_64(trg_data, (uint64_t *)&multiplier) != + if(trg_swap_byte_order_64(trg_data, (int64_t *)&multiplier) != TRG_SUCCESS) { printf("Cannot swap byte order to get big endian. %s: %d\n", @@ -4364,8 +4364,8 @@ static trg_function_status trg_read_data_block_contents static trg_function_status trg_update_md5_hash(struct trg_trajectory *trg_data, struct trg_gen_block *block, - uint64_t header_start_pos, - uint64_t contents_start_pos) + int64_t header_start_pos, + int64_t contents_start_pos) { if(block->block_contents) { @@ -4383,7 +4383,7 @@ static trg_function_status trg_update_md5_hash(struct trg_trajectory *trg_data, trg_generate_block_hash(block); - fseek(trg_data->output_file, header_start_pos + 3 * sizeof(uint64_t), + fseek(trg_data->output_file, header_start_pos + 3 * sizeof(int64_t), SEEK_SET); fwrite(block->hash, TRG_HASH_LEN, 1, trg_data->output_file); @@ -4396,7 +4396,7 @@ static trg_function_status trg_update_header_pointers { struct trg_gen_block block; FILE *temp = trg_data->input_file; - uint64_t pos, contents_start_pos; + int64_t pos, contents_start_pos; if(trg_init_output_file(trg_data, FALSE) != TRG_SUCCESS) { @@ -4424,7 +4424,7 @@ static trg_function_status trg_update_header_pointers contents_start_pos = ftell(trg_data->output_file); fseek(trg_data->output_file, block.block_contents_size - 3 * - sizeof(uint64_t), SEEK_CUR); + sizeof(int64_t), SEEK_CUR); trg_data->input_file = temp; @@ -4443,7 +4443,7 @@ static trg_function_status trg_update_header_pointers } } - if(fwrite(&pos, sizeof(uint64_t), 1, trg_data->output_file) != 1) + if(fwrite(&pos, sizeof(int64_t), 1, trg_data->output_file) != 1) { trg_destroy_block(&block); return(TRG_CRITICAL); @@ -4464,7 +4464,7 @@ static trg_function_status trg_update_header_pointers } if(fwrite(&pos, - sizeof(uint64_t), 1, trg_data->output_file) != 1) + sizeof(int64_t), 1, trg_data->output_file) != 1) { trg_destroy_block(&block); return(TRG_CRITICAL); @@ -4485,7 +4485,7 @@ static trg_function_status trg_update_frame_set_pointers struct trg_gen_block block; struct trg_trajectory_frame_set *frame_set; FILE *temp = trg_data->input_file; - uint64_t pos, header_start_pos, contents_start_pos; + int64_t pos, header_start_pos, contents_start_pos; if(trg_init_output_file(trg_data, FALSE) != TRG_SUCCESS) { @@ -4500,7 +4500,7 @@ static trg_function_status trg_update_frame_set_pointers trg_data->input_file = trg_data->output_file; frame_set = &trg_data->current_trajectory_frame_set; - if(frame_set->prev_frame_set_file_pos != -1ULL && + if(frame_set->prev_frame_set_file_pos != -1 && frame_set->prev_frame_set_file_pos != 0) { fseek(trg_data->output_file, frame_set->prev_frame_set_file_pos, @@ -4520,7 +4520,7 @@ static trg_function_status trg_update_frame_set_pointers contents_start_pos = ftell(trg_data->output_file); fseek(trg_data->output_file, block.block_contents_size - 4 * - sizeof(uint64_t), SEEK_CUR); + sizeof(int64_t), SEEK_CUR); // printf("Updating frame set\n"); // printf("%ld: Next frame set %ld\n", ftell(trg_data->output_file), @@ -4537,7 +4537,7 @@ static trg_function_status trg_update_frame_set_pointers } } - if(fwrite(&pos, sizeof(uint64_t), 1, trg_data->output_file) != 1) + if(fwrite(&pos, sizeof(int64_t), 1, trg_data->output_file) != 1) { trg_destroy_block(&block); trg_data->input_file = temp; @@ -4550,7 +4550,7 @@ static trg_function_status trg_update_frame_set_pointers fseek(trg_data->output_file, trg_data->output_file_pos, SEEK_SET); } - if(frame_set->long_stride_prev_frame_set_file_pos != -1ULL && + if(frame_set->long_stride_prev_frame_set_file_pos != -1 && frame_set->long_stride_prev_frame_set_file_pos != 0) { fseek(trg_data->output_file, @@ -4569,7 +4569,7 @@ static trg_function_status trg_update_frame_set_pointers contents_start_pos = ftell(trg_data->output_file); fseek(trg_data->output_file, block.block_contents_size - 2 * - sizeof(uint64_t), SEEK_CUR); + sizeof(int64_t), SEEK_CUR); pos = trg_data->current_trajectory_frame_set_output_file_pos; @@ -4582,7 +4582,7 @@ static trg_function_status trg_update_frame_set_pointers } } - if(fwrite(&pos, sizeof(uint64_t), 1, trg_data->output_file) != 1) + if(fwrite(&pos, sizeof(int64_t), 1, trg_data->output_file) != 1) { trg_destroy_block(&block); trg_data->input_file = temp; @@ -4770,7 +4770,7 @@ trg_function_status trg_add_molecule(struct trg_trajectory *trg_data, struct trg_molecule **molecule) { struct trg_molecule *new_molecules; - uint64_t *new_molecule_cnt_list; + int64_t *new_molecule_cnt_list; int id, i; trg_bool found_id = TRUE; @@ -4786,14 +4786,14 @@ trg_function_status trg_add_molecule(struct trg_trajectory *trg_data, return(TRG_CRITICAL); } - new_molecule_cnt_list = (uint64_t *) realloc(trg_data->molecule_cnt_list, - sizeof(uint64_t) * + new_molecule_cnt_list = (int64_t *) realloc(trg_data->molecule_cnt_list, + sizeof(int64_t) * (trg_data->n_molecules + 1)); if(!new_molecules) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - sizeof(uint64_t) * (trg_data->n_molecules + 1), + sizeof(int64_t) * (trg_data->n_molecules + 1), __FILE__, __LINE__); return(TRG_CRITICAL); } @@ -4866,7 +4866,7 @@ trg_function_status trg_set_molecule_name(struct trg_trajectory *trg_data, trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - uint64_t *cnt) + int64_t *cnt) { int i, index = -1; @@ -4889,7 +4889,7 @@ trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, trg_function_status trg_set_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - const uint64_t cnt) + const int64_t cnt) { int i, index = -1, old_cnt; @@ -5326,7 +5326,7 @@ trg_function_status trg_init_trajectory(struct trg_trajectory *trg_data) trg_data->id_name_pairs = 0; /* Check the endianness of the computer */ - static uint32_t endianness_32 = 0x01234567; + static int32_t endianness_32 = 0x01234567; /* 0x01234567 */ if ( *(const uint8_t*)&endianness_32 == 0x01 ) { @@ -5346,7 +5346,7 @@ trg_function_status trg_init_trajectory(struct trg_trajectory *trg_data) trg_data->endianness_32 = TRG_BYTE_PAIR_SWAP_32; } - static uint64_t endianness_64 = 0x0123456789ABCDEF; + static int64_t endianness_64 = 0x0123456789ABCDEF; /* 0x0123456789ABCDEF */ if ( *(const uint8_t*)&endianness_64 == 0x01 ) { @@ -5396,7 +5396,7 @@ trg_function_status trg_init_trajectory(struct trg_trajectory *trg_data) trg_function_status trg_destroy_trajectory(struct trg_trajectory *trg_data) { - uint64_t n_frames, n_particles; + int64_t n_frames, n_particles; int i, j, k, l; struct trg_trajectory_frame_set *frame_set = &trg_data->current_trajectory_frame_set; @@ -6343,15 +6343,15 @@ trg_function_status trg_write_frame_set(struct trg_trajectory *trg_data, } trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, - const uint64_t first_frame, - const uint64_t n_frames) + const int64_t first_frame, + const int64_t n_frames) { int i; struct trg_gen_block block; struct trg_trajectory_frame_set *frame_set; struct trg_particle_mapping *mapping; FILE *temp = trg_data->input_file; - uint64_t curr_pos; + int64_t curr_pos; frame_set = &trg_data->current_trajectory_frame_set; @@ -6399,7 +6399,7 @@ trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, { /* FIXME: Currently only working if the previous frame set has its * long stride pointer already set. This might need some fixing. */ - if(frame_set->long_stride_prev_frame_set_file_pos != -1ULL && + if(frame_set->long_stride_prev_frame_set_file_pos != -1 && frame_set->long_stride_prev_frame_set_file_pos != 0) { trg_init_block(&block); @@ -6422,7 +6422,7 @@ trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, /* Read the next frame set from the previous frame set and one * long stride step back */ fseek(trg_data->output_file, block.block_contents_size - 4 * - sizeof(uint64_t), SEEK_CUR); + sizeof(int64_t), SEEK_CUR); if(fread(&frame_set->long_stride_prev_frame_set_file_pos, sizeof(frame_set->long_stride_prev_frame_set_file_pos), 1, trg_data->output_file) == 0) @@ -6456,7 +6456,7 @@ trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, // frame_set->n_particle_data_blocks = 0; // frame_set->n_data_blocks = 0; - if(trg_data->first_trajectory_frame_set_output_file_pos == -1ULL || + if(trg_data->first_trajectory_frame_set_output_file_pos == -1 || trg_data->first_trajectory_frame_set_output_file_pos == 0) { trg_data->first_trajectory_frame_set_output_file_pos = @@ -6464,7 +6464,7 @@ trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, } /* FIXME: Should check the frame number instead of the file_pos, * in case frame sets are not in order */ - if(trg_data->last_trajectory_frame_set_output_file_pos == -1ULL || + if(trg_data->last_trajectory_frame_set_output_file_pos == -1 || trg_data->last_trajectory_frame_set_output_file_pos == 0 || trg_data->last_trajectory_frame_set_output_file_pos < trg_data->current_trajectory_frame_set_output_file_pos) @@ -6478,13 +6478,13 @@ trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, /* UNTESTED */ trg_function_status trg_add_data_block(struct trg_trajectory *trg_data, - const uint64_t id, + const int64_t id, const char *block_name, const char datatype, - const uint64_t n_frames, - const uint64_t n_values_per_frame, - const uint64_t stride_length, - uint64_t codec_id, + const int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + int64_t codec_id, void *new_data) { int i, j, block_index, size, len; @@ -6588,7 +6588,7 @@ trg_function_status trg_add_data_block(struct trg_trajectory *trg_data, size = sizeof(float); break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_CHAR_DATA: size = sizeof(char); @@ -6652,19 +6652,19 @@ trg_function_status trg_add_data_block(struct trg_trajectory *trg_data, trg_function_status trg_add_particle_data_block(struct trg_trajectory *trg_data, - const uint64_t id, + const int64_t id, const char *block_name, const char datatype, - const uint64_t n_frames, - const uint64_t n_values_per_frame, - const uint64_t stride_length, - const uint64_t first_particle_number, - const uint64_t n_particles, - uint64_t codec_id, + const int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + const int64_t first_particle_number, + const int64_t n_particles, + int64_t codec_id, void *new_data) { int i, j, k, block_index, size, len; - uint64_t tot_n_particles; + int64_t tot_n_particles; struct trg_trajectory_frame_set *frame_set; struct trg_particle_data *data; void *orig; @@ -6778,7 +6778,7 @@ trg_function_status trg_add_particle_data_block(struct trg_trajectory *trg_data, size = sizeof(float); break; case TRG_INT_DATA: - size = sizeof(uint64_t); + size = sizeof(int64_t); break; case TRG_CHAR_DATA: size = sizeof(char); @@ -6859,7 +6859,7 @@ trg_function_status trg_write_next_traj_block(struct trg_trajectory *trg_data, } trg_function_status trg_read_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file) { /* STUB */ @@ -6867,7 +6867,7 @@ trg_function_status trg_read_traj_block(struct trg_trajectory *trg_data, } trg_function_status trg_write_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file) { /* STUB */ @@ -6875,7 +6875,7 @@ trg_function_status trg_write_traj_block(struct trg_trajectory *trg_data, } trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file) { /* STUB */ @@ -6883,7 +6883,7 @@ trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_data, } trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file) { /* STUB */ @@ -6891,8 +6891,8 @@ trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_data, } trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file) { /* STUB */ @@ -6900,8 +6900,8 @@ trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_data, } trg_function_status trg_write_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file) { /* STUB */ @@ -6909,7 +6909,7 @@ trg_function_status trg_write_frame_nrs(struct trg_trajectory *trg_data, } trg_function_status trg_read_frame_set_nr(struct trg_trajectory *trg_data, - uint64_t frame_set_nr) + int64_t frame_set_nr) { return(TRG_SUCCESS); } diff --git a/src/lib/trg_io.h b/src/lib/trg_io.h index 7bdca5e..d321e6e 100644 --- a/src/lib/trg_io.h +++ b/src/lib/trg_io.h @@ -88,44 +88,44 @@ extern "C" #endif struct trg_bond { - uint64_t from_atom_id; /* One of the atoms of the bond */ - uint64_t to_atom_id; /* The other atom of the bond */ + int64_t from_atom_id; /* One of the atoms of the bond */ + int64_t to_atom_id; /* The other atom of the bond */ }; struct trg_atom { struct trg_residue *residue; /* The molecule containing this atom */ - uint64_t id; /* A unique (per molecule) ID number of the atom */ + int64_t id; /* A unique (per molecule) ID number of the atom */ char *atom_type; /* The atom_type (depending on the forcefield) */ char *name; /* The name of the atom */ }; struct trg_residue { struct trg_chain *chain; /* The chain containing this residue */ - uint64_t id; /* A unique (per chain) ID number of the residue */ + int64_t id; /* A unique (per chain) ID number of the residue */ char *name; /* The name of the residue */ - uint64_t n_atoms; /* The number of atoms in the residue */ + int64_t n_atoms; /* The number of atoms in the residue */ struct trg_atom *atoms; /* A list of atoms in the residue */ }; struct trg_chain { struct trg_molecule *molecule; /* The molecule containing this chain */ - uint64_t id; /* A unique (per molecule) ID number of the chain */ + int64_t id; /* A unique (per molecule) ID number of the chain */ char *name; /* The name of the chain */ - uint64_t n_residues; /* The number of residues in the chain */ + int64_t n_residues; /* The number of residues in the chain */ struct trg_residue *residues; /* A list of residues in the chain */ }; struct trg_molecule { - uint64_t id; /* A unique ID number of the molecule */ - uint64_t quaternary_str; /* Quaternary structure of the molecule. + int64_t id; /* A unique ID number of the molecule */ + int64_t quaternary_str; /* Quaternary structure of the molecule. 1 => monomeric 2 => dimeric 3 => trimeric etc */ - uint64_t n_chains; /* The number of chains in the molecule */ - uint64_t n_residues; /* The number of residues in the molecule */ - uint64_t n_atoms; /* The number of atoms in the molecule */ - uint64_t n_bonds; /* The number of bonds in the molecule. + int64_t n_chains; /* The number of chains in the molecule */ + int64_t n_residues; /* The number of residues in the molecule */ + int64_t n_atoms; /* The number of atoms in the molecule */ + int64_t n_bonds; /* The number of bonds in the molecule. If the bonds are not specified this value can be 0. */ char *name; /* The name of the molecule */ @@ -136,51 +136,51 @@ struct trg_molecule { }; struct trg_gen_block { - uint64_t header_contents_size; /* The size of the block header in bytes */ - uint64_t block_contents_size; /* The size of the block contents in bytes */ - uint64_t id; /* The ID of the block to determine its type */ + int64_t header_contents_size; /* The size of the block header in bytes */ + int64_t block_contents_size; /* The size of the block contents in bytes */ + int64_t id; /* The ID of the block to determine its type */ char hash[TRG_HASH_LEN]; /* The MD5 hash of the block to verify integrity */ char *name; /* The name of the block */ - uint64_t block_version; /* The library version used to write the block */ + int64_t block_version; /* The library version used to write the block */ char *header_contents; /* The full block header contents */ char *block_contents; /* The full block contents */ }; struct trg_frame_set_toc { - uint64_t n_blocks; /* The number of blocks listed in this + int64_t n_blocks; /* The number of blocks listed in this table of contents */ char **block_names; /* A list of block names */ }; struct trg_particle_mapping { - uint64_t num_first_particle; /* The index number of the first particle + int64_t num_first_particle; /* The index number of the first particle in this mapping block */ - uint64_t n_particles; /* The number of particles list in this + int64_t n_particles; /* The number of particles list in this mapping block */ - uint64_t *real_particle_numbers; /* the mapping of index numbers to the + int64_t *real_particle_numbers; /* the mapping of index numbers to the real particle numbers in the trajectory */ }; struct trg_trajectory_frame_set { struct trg_frame_set_toc contents; /* The table of contents of this frame set */ - uint64_t n_mapping_blocks; /* The number of different particle + int64_t n_mapping_blocks; /* The number of different particle mapping blocks present. */ struct trg_particle_mapping *mappings; /* The atom mappings of this frame set */ - uint64_t first_frame; /* The first frame of this frame set */ - uint64_t n_frames; /* The number of frames in this frame set */ - uint64_t *molecule_cnt_list; /* A list of the number of each molecule + int64_t first_frame; /* The first frame of this frame set */ + int64_t n_frames; /* The number of frames in this frame set */ + int64_t *molecule_cnt_list; /* A list of the number of each molecule type - only used when using variable number of atoms */ - uint64_t n_particles; /* The number of particles/atoms - only + int64_t n_particles; /* The number of particles/atoms - only used when using variable number of atoms */ - uint64_t next_frame_set_file_pos; /* The file position of the next frame set */ - uint64_t prev_frame_set_file_pos; /* The file position of the previous + int64_t next_frame_set_file_pos; /* The file position of the next frame set */ + int64_t prev_frame_set_file_pos; /* The file position of the previous frame set */ - uint64_t long_stride_next_frame_set_file_pos; /* The file position of the frame + int64_t long_stride_next_frame_set_file_pos; /* The file position of the frame set one stride step ahead */ - uint64_t long_stride_prev_frame_set_file_pos; /* The file position of the frame + int64_t long_stride_prev_frame_set_file_pos; /* The file position of the frame set one stride step behind */ /* The data blocks in a frame set are trajectory data blocks */ @@ -203,7 +203,7 @@ union data_values { /* FIXME: Should there be a pointer to a trg_gen_block from each data block? */ struct trg_particle_data { - uint64_t block_id; /* The block ID of the data block + int64_t block_id; /* The block ID of the data block containing this particle data. This is used to determine the kind of data that is stored */ @@ -211,16 +211,16 @@ struct trg_particle_data { This is used to determine the kind of data that is stored */ trg_data_type datatype; /* The type of data stored. */ - uint64_t first_frame_with_data; /* The first frame number of the + int64_t first_frame_with_data; /* The first frame number of the first data point */ - uint64_t n_frames; /* The number of frames in this + int64_t n_frames; /* The number of frames in this frame set */ - uint64_t n_values_per_frame; /* The number of values stored per + int64_t n_values_per_frame; /* The number of values stored per frame */ - uint64_t stride_length; /* The number of frames between + int64_t stride_length; /* The number of frames between each data point - e.g. when storing sparse data. */ - uint64_t codec_id; /* ID of the CODEC used for compression + int64_t codec_id; /* ID of the CODEC used for compression 0 == no compression. */ double compression_multiplier; /* The multiplier used for getting integer values for compression */ @@ -230,16 +230,16 @@ struct trg_particle_data { }; struct trg_data { - uint64_t block_id; + int64_t block_id; char *block_name; /* The name of the data block. This is used to determine the kind of data that is stored */ trg_data_type datatype; /* The type of data stored. */ - uint64_t first_frame_with_data; - uint64_t n_frames; - uint64_t n_values_per_frame; - uint64_t stride_length; - uint64_t codec_id; /* ID of the CODEC used for compression + int64_t first_frame_with_data; + int64_t n_frames; + int64_t n_values_per_frame; + int64_t stride_length; + int64_t codec_id; /* ID of the CODEC used for compression 0 == no compression. */ double compression_multiplier; union data_values **values; /* A 2-dimensional array of values, @@ -267,7 +267,7 @@ struct trg_trajectory { char *forcefield_name; /* The forcefield used in the simulations */ char *user_name; /* The name of the user running the simulations */ - uint64_t time; /* The time (n seconds since 1970) when + int64_t time; /* The time (n seconds since 1970) when the file was created */ char *computer_name; /* The name of the computer on which the simulations were performed */ @@ -276,38 +276,38 @@ struct trg_trajectory { char var_num_atoms_flag; /* A flag indicating if the number of atoms can vary throughout the simulation, e.g. using a grand canonical ensemble */ - uint64_t frame_set_n_frames; /* The number of frames in a frame set. + int64_t frame_set_n_frames; /* The number of frames in a frame set. It is allowed to have frame sets with fewer frames, but this will help searching for specific frames */ - uint64_t stride_length; /* The number of frame sets in a long stride + int64_t stride_length; /* The number of frame sets in a long stride step */ - uint64_t n_molecules; /* The number of different kinds of + int64_t n_molecules; /* The number of different kinds of molecules in the trajectory */ struct trg_molecule *molecules; /* A list of molecules in the trajectory */ - uint64_t *molecule_cnt_list; /* A list of the count of each molecule - + int64_t *molecule_cnt_list; /* A list of the count of each molecule - if using variable number of particles this will be specified in each frame set */ - uint64_t n_particles; /* The total number of particles/atoms. If + int64_t n_particles; /* The total number of particles/atoms. If using variable number of particles this will be specified in each frame set */ - uint64_t n_id_name_pairs; /* The number of ID-name + int64_t n_id_name_pairs; /* The number of ID-name pairs */ struct trg_block_id_name_pair *id_name_pairs; /* A list of ID-name pairs */ - uint64_t first_trajectory_frame_set_input_file_pos; /* The pos in the src + int64_t first_trajectory_frame_set_input_file_pos; /* The pos in the src file of the first frame set */ - uint64_t first_trajectory_frame_set_output_file_pos; /* The pos in the dest + int64_t first_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the first frame set */ - uint64_t last_trajectory_frame_set_input_file_pos; /* The pos in the src + int64_t last_trajectory_frame_set_input_file_pos; /* The pos in the src file of the last frame set */ - uint64_t last_trajectory_frame_set_output_file_pos; /* The pos in the dest + int64_t last_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the last frame set */ struct trg_trajectory_frame_set current_trajectory_frame_set; /* The currently @@ -319,12 +319,12 @@ struct trg_trajectory { long int current_trajectory_frame_set_output_file_pos;/* The pos in the dest file of the current frame set */ - uint64_t n_trajectory_frame_sets; /* The number of frame sets + int64_t n_trajectory_frame_sets; /* The number of frame sets in the trajectory */ - uint64_t n_trajectory_blocks; /* The number of trajectory blocks + int64_t n_trajectory_blocks; /* The number of trajectory blocks in the file */ - uint64_t n_non_trajectory_blocks; /* The number of non-trajectory blocks + int64_t n_non_trajectory_blocks; /* The number of non-trajectory blocks in the file */ struct trg_gen_block non_trajectory_blocks[32]; /* A list of non-trajectory blocks */ @@ -471,7 +471,7 @@ trg_function_status trg_set_molecule_name(struct trg_trajectory *trg_data, has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - uint64_t *cnt); + int64_t *cnt); /* Set the count of a molecule. *trg_data is a pointer to the trajectory containing the molecule. @@ -481,7 +481,7 @@ trg_function_status trg_get_molecule_cnt(struct trg_trajectory *trg_data, has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_set_molecule_cnt(struct trg_trajectory *trg_data, struct trg_molecule *molecule, - uint64_t cnt); + int64_t cnt); /* Add a chain to a molecule. *trg_data is a pointer to the trajectory containing the molecule. @@ -632,19 +632,19 @@ trg_function_status trg_write_frame_set(struct trg_trajectory *trg_data, trg_close_file_flag close_file); trg_function_status trg_new_frame_set(struct trg_trajectory *trg_data, - const uint64_t first_frame, - const uint64_t n_frames); + const int64_t first_frame, + const int64_t n_frames); trg_function_status trg_add_particle_data_block(struct trg_trajectory *trg_data, - const uint64_t id, + const int64_t id, const char *block_name, const char datatype, - const uint64_t n_frames, - const uint64_t n_values_per_frame, - const uint64_t stride_length, - const uint64_t first_particle_number, - const uint64_t n_particles, - uint64_t codec_id, + const int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + const int64_t first_particle_number, + const int64_t n_particles, + int64_t codec_id, void *new_data); @@ -674,7 +674,7 @@ trg_function_status trg_write_next_traj_block(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_read_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file); /* Write one trajectory block to the output_file of trg_data. @@ -685,7 +685,7 @@ trg_function_status trg_read_traj_block(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_write_traj_block(struct trg_trajectory *trg_data, - uint64_t block_id, + int64_t block_id, trg_close_file_flag close_file); /* Read a requested frame set. @@ -695,7 +695,7 @@ trg_function_status trg_write_traj_block(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_read_frame_set_nr(struct trg_trajectory *trg_data, - uint64_t frame_set_nr); + int64_t frame_set_nr); /* Read one trajectory frame from the input_file of trg_data. *trg_data is a pointer to trajectory data. trg_data->input_file_path specifies which @@ -705,7 +705,7 @@ trg_function_status trg_read_frame_set_nr(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file); /* Write one trajectory frame to the output_file of trg_data. @@ -716,7 +716,7 @@ trg_function_status trg_read_frame_nr(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_data, - uint64_t frame_nr, + int64_t frame_nr, trg_close_file_flag close_file); /* Read a number of consecutive trajectory frames from the input_file of trg_data. @@ -728,8 +728,8 @@ trg_function_status trg_write_frame_nr(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file); /* Write a number of consecutive trajectory frames to the output_file of trg_data. @@ -741,8 +741,8 @@ trg_function_status trg_read_frame_nrs(struct trg_trajectory *trg_data, Returns TRG_SUCCESS (0) if successful, TRG_FAILURE (1) if a minor error has occurred or TRG_CRITICAL (2) if a major error has occured. */ trg_function_status trg_write_frame_nrs(struct trg_trajectory *trg_data, - uint64_t start_frame_nr, - uint64_t end_frame_nr, + int64_t start_frame_nr, + int64_t end_frame_nr, trg_close_file_flag close_file); /* Get the date and time of initial file creation in ISO format (string). diff --git a/src/tests/trg_io_testing.c b/src/tests/trg_io_testing.c index caa74dd..08a2b90 100644 --- a/src/tests/trg_io_testing.c +++ b/src/tests/trg_io_testing.c @@ -12,7 +12,7 @@ static trg_function_status trg_setup_test_molecules(struct trg_trajectory *traj) struct trg_chain *chain; struct trg_residue *residue; struct trg_atom *atom; - uint64_t cnt; + int64_t cnt; // int i; trg_add_molecule(traj, "water", &molecule); |