#ifndef _TNGIO_H #define _TNGIO_H 1 #include #include #define TNG_VERSION 1 #define TNG_PARTICLE_DEPENDENT 1 #define TNG_FRAME_DEPENDENT 2 // #define TNG_MAX_BLOCK_PARTICLES 1000 #define TNG_MAX_DATE_STR_LEN 24 #define TNG_HASH_LEN 16 #define TNG_MAX_STR_LEN 1024 typedef enum {TNG_BIG_ENDIAN_32, TNG_LITTLE_ENDIAN_32, TNG_BYTE_PAIR_SWAP_32} tng_endianness_32; typedef enum {TNG_BIG_ENDIAN_64, TNG_LITTLE_ENDIAN_64, TNG_QUAD_SWAP_64, TNG_BYTE_PAIR_SWAP_64, TNG_BYTE_SWAP_64} tng_endianness_64; #define min(a,b) \ ({ __typeof__ (a) _a = (a); \ __typeof__ (b) _b = (b); \ _a < _b ? _a : _b; }) #define max(a,b) \ ({ __typeof__ (a) _a = (a); \ __typeof__ (b) _b = (b); \ _a > _b ? _a : _b; }) typedef enum {TNG_UNCOMPRESSED, TNG_XTC_COMPRESSION, TNG_TNG_COMPRESSION} tng_compression; typedef enum {TNG_NON_TRAJECTORY_BLOCK, TNG_TRAJECTORY_BLOCK} tng_block_type; typedef enum {TNG_ENDIANNESS_AND_STRING_LENGTH, TNG_GENERAL_INFO, TNG_MOLECULES, TNG_TRAJECTORY_IDS_AND_NAMES, TNG_TRAJECTORY_FRAME_SET, TNG_BLOCK_TABLE_OF_CONTENTS, TNG_PARTICLE_MAPPING} tng_non_trajectory_block_ids; typedef enum {TNG_TRAJ_BOX_SHAPE = 10000, TNG_TRAJ_POSITIONS, TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES} tng_trajectory_block_ids; typedef enum {TNG_NON_PARTICLE_BLOCK_DATA, TNG_PARTICLE_BLOCK_DATA} tng_particle_block_data; /*typedef enum {TNG_NO_HASH, TNG_OTHER_HASH, TNG_MD5_HASH, TNG_MD6_HASH, TNG_SHA0_HASH, TNG_SHA1_HASH, TNG_SHA256_HASH, TNG_SHA512_HASH} tng_hash_type;*/ typedef enum {FALSE, TRUE} tng_bool; typedef enum {TNG_CONSTANT_N_ATOMS, TNG_VARIABLE_N_ATOMS} tng_variable_n_atoms_flag; typedef enum {TNG_SUCCESS, TNG_FAILURE, TNG_CRITICAL} tng_function_status; typedef enum {TNG_NORMAL_WRITE, TNG_COPY_EXISTING} tng_write_mode; typedef enum {TNG_SKIP_HASH, TNG_USE_HASH} tng_hash_mode; typedef enum {TNG_CHAR_DATA, TNG_INT_DATA, TNG_FLOAT_DATA, TNG_DOUBLE_DATA} tng_data_type; typedef struct tng_trajectory *tng_trajectory_t; typedef struct tng_molecule *tng_molecule_t; typedef struct tng_chain *tng_chain_t; typedef struct tng_residue *tng_residue_t; typedef struct tng_atom *tng_atom_t; typedef struct tng_bond *tng_bond_t; #ifdef __cplusplus extern "C" { #endif struct tng_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 tng_atom { tng_residue_t residue; /* The molecule containing this 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 tng_residue { tng_chain_t chain; /* The chain containing this residue */ int64_t id; /* A unique (per chain) ID number of the residue */ char *name; /* The name of the residue */ int64_t n_atoms; /* The number of atoms in the residue */ tng_atom_t atoms; /* A list of atoms in the residue */ }; struct tng_chain { tng_molecule_t molecule; /* The molecule containing this chain */ int64_t id; /* A unique (per molecule) ID number of the chain */ char *name; /* The name of the chain */ int64_t n_residues; /* The number of residues in the chain */ tng_residue_t residues; /* A list of residues in the chain */ }; struct tng_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 */ 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 */ tng_chain_t chains; /* A list of chains in the molecule */ tng_residue_t residues; /* A list of residues in the molecule */ tng_atom_t atoms; /* A list of the atoms in the molecule */ tng_bond_t bonds; /* A list of the bonds in the molecule */ }; struct tng_gen_block { 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[TNG_HASH_LEN]; /* The MD5 hash of the block to verify integrity */ char *name; /* The name of 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 tng_frame_set_toc { int64_t n_blocks; /* The number of blocks listed in this table of contents */ char **block_names; /* A list of block names */ }; struct tng_particle_mapping { int64_t num_first_particle; /* The index number of the first particle in this mapping block */ int64_t n_particles; /* The number of particles list in this mapping block */ int64_t *real_particle_numbers; /* the mapping of index numbers to the real particle numbers in the trajectory */ }; struct tng_trajectory_frame_set { struct tng_frame_set_toc contents; /* The table of contents of this frame set */ int64_t n_mapping_blocks; /* The number of different particle mapping blocks present. */ struct tng_particle_mapping *mappings; /* The atom mappings of this frame set */ 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 */ int64_t n_particles; /* The number of particles/atoms - only used when using variable number of atoms */ 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 */ int64_t long_stride_next_frame_set_file_pos; /* The file position of the frame set one stride step ahead */ 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 */ int n_particle_data_blocks; /* The number of data blocks of particle dependent data */ struct tng_particle_data *tr_particle_data; /* A list of data blocks containing particle dependent data */ int n_data_blocks; struct tng_data *tr_data; }; /* Data can be either double, float, int or a string */ union data_values { double d; float f; int i; char *c; }; /* FIXME: Should there be a pointer to a tng_gen_block from each data block? */ struct tng_particle_data { 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 */ char *block_name; /* The name of the data block. This is used to determine the kind of data that is stored */ tng_data_type datatype; /* The type of data stored. */ int64_t first_frame_with_data; /* The first frame number of the first data point */ int64_t n_frames; /* The number of frames in this frame set */ int64_t n_values_per_frame; /* The number of values stored per frame */ int64_t stride_length; /* The number of frames between each data point - e.g. when storing sparse data. */ 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 */ union data_values ***values; /* A 3-dimensional array of values, sized n_frames x n_particles x n_values_per_frame */ }; struct tng_data { 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 */ tng_data_type datatype; /* The type of data stored. */ 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, sized n_frames x n_values_per_frame */ }; struct tng_trajectory { char *input_file_path; /* The path of the input trajectory file */ FILE *input_file; /* A handle to the input file */ long int input_file_pos; /* The reading position of the file */ long int input_file_len; /* The length of the input file */ char *output_file_path; /* The path of the output trajectory file */ FILE *output_file; /* A handle to the output file */ long int output_file_pos; /* The writing position of the file */ tng_endianness_32 endianness_32; /* The endianness of 32 bit values of the current computer */ tng_endianness_64 endianness_64; /* The endianness of 64 bit values of the current computer */ char *program_name; /* The name of the program producing this trajectory */ char *forcefield_name; /* The forcefield used in the simulations */ char *user_name; /* The name of the user running the simulations */ 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 */ char *pgp_signature; /* The PGP signature of the user creating the file. */ 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 */ 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 */ int64_t stride_length; /* The number of frame sets in a long stride step */ int64_t n_molecules; /* The number of different kinds of molecules in the trajectory */ tng_molecule_t molecules; /* A list of molecules in the trajectory */ 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 */ int64_t n_particles; /* The total number of particles/atoms. If using variable number of particles this will be specified in each frame set */ int64_t n_id_name_pairs; /* The number of ID-name pairs */ struct tng_block_id_name_pair *id_name_pairs; /* A list of ID-name pairs */ int64_t first_trajectory_frame_set_input_file_pos; /* The pos in the src file of the first frame set */ int64_t first_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the first frame set */ int64_t last_trajectory_frame_set_input_file_pos; /* The pos in the src file of the last frame set */ int64_t last_trajectory_frame_set_output_file_pos; /* The pos in the dest file of the last frame set */ struct tng_trajectory_frame_set current_trajectory_frame_set; /* The currently active frame set */ long int current_trajectory_frame_set_input_file_pos; /* The pos in the src file of the current frame set */ long int current_trajectory_frame_set_output_file_pos;/* The pos in the dest file of the current frame set */ int64_t n_trajectory_frame_sets; /* The number of frame sets in the trajectory */ int64_t n_trajectory_blocks; /* The number of trajectory blocks in the file */ int64_t n_non_trajectory_blocks; /* The number of non-trajectory blocks in the file */ struct tng_gen_block non_trajectory_blocks[32]; /* A list of non-trajectory blocks */ /* These data blocks are non-trajectory data blocks */ int n_particle_data_blocks; /* The number of non-frame dependent particle dependent data blocks */ struct tng_particle_data *non_tr_particle_data; /* A list of data blocks containing particle dependent data */ int n_data_blocks; /* The number of frame and particle independent data blocks */ struct tng_data *non_tr_data; /* A list of frame and particle indepdendent data blocks */ }; /* Setup a trajectory data container. *tng_data is a pointer to pre-allocated memory. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_trajectory_init(tng_trajectory_t tng_data); /* Clean up a trajectory data container. *tng_data is a pointer to pre-allocated memory containing trajectory data. All allocated memory in the data structure is freed. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_trajectory_destroy(tng_trajectory_t tng_data); /* Set the name of the input file. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_input_file_set(tng_trajectory_t tng_data, const char *file_name); /* Set the name of the output file. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_output_file_set(tng_trajectory_t tng_data, const char *file_name); /* Set the program name used when creating the trajectory. *tng_data is a pointer to pre-allocated memory containing trajectory data. *new_name is a pointer to the string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_program_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the forcefield used in the trajectory. *tng_data is a pointer to pre-allocated memory containing trajectory data. *new_name is a pointer to the string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_forcefield_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the user creating the trajectory. *tng_data is a pointer to pre-allocated memory containing trajectory data. *new_name is a pointer to the string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_user_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the name of the computer used when creating the trajectory. *tng_data is a pointer to pre-allocated memory containing trajectory data. *new_name is a pointer to the string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_computer_name_set(tng_trajectory_t tng_data, const char *new_name); /* Set the pgp_signature of the trajectory. *tng_data is a pointer to pre-allocated memory containing trajectory data. *signature is a pointer to the string containing the pgp_signature. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_signature_set(tng_trajectory_t tng_data, const char *signature); /* Setup a molecule container. *molecule is a pointer to pre-allocated memory. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_init(tng_molecule_t molecule); /* Clean up a molecule container. *molecule is a pointer to pre-allocated memory containing a molecule. All allocated memory in the data structure is freed. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_destroy(tng_molecule_t molecule); /* Setup a data block. *block is a pointer to pre-allocated memory. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_block_init(struct tng_gen_block *block); /* Clean up a data block. *block is a pointer to pre-allocated memory. All allocated memory in the data structure is freed. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_block_destroy(struct tng_gen_block *block); /* Set the name of a data block. tng_data is the trajectory data container containing the block.. *block is a pointer to the block to rename. *new_name is a string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_block_name_set(tng_trajectory_t tng_data, struct tng_gen_block *block, const char *new_name); /* Add a molecule to the trajectory. tng_data is the trajectory data container containing the block.. *name is a pointer to the string containing the name of the new molecule. **molecule is a pointer to a pointer to the newly created molecule. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_add(tng_trajectory_t tng_data, const char *name, tng_molecule_t *molecule); /* Set the name of a molecule. tng_data is the trajectory data container containing the molecule.. *molecule is a pointer to the molecule to rename. *new_name is a string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_name_set(tng_trajectory_t tng_data, tng_molecule_t molecule, const char *new_name); /* Set the count of a molecule. tng_data is the trajectory data container containing the molecule.. *molecule is a pointer to the molecule to rename. *cnt is a pointer to the variable to be populated with the count. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_cnt_get(tng_trajectory_t tng_data, tng_molecule_t molecule, int64_t *cnt); /* Set the count of a molecule. tng_data is the trajectory data container containing the molecule.. *molecule is a pointer to the molecule to rename. cnt is the number of instances of this molecule. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_cnt_set(tng_trajectory_t tng_data, tng_molecule_t molecule, int64_t cnt); /* Add a chain to a molecule. tng_data is the trajectory data container containing the molecule.. *molecule is a pointer to the molecule to add a chain to. *name is a pointer to a string containing the name of the chain. **chain is a pointer to a pointer to the newly created chain. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_molecule_chain_add(tng_trajectory_t tng_data, tng_molecule_t molecule, const char *name, tng_chain_t *chain); /* Set the name of a chain. tng_data is the trajectory data container containing the atom.. *chain is a pointer to the chain to rename. *new_name is a string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_chain_name_set(tng_trajectory_t tng_data, tng_chain_t chain, const char *new_name); /* Add a residue to a chain. tng_data is the trajectory data container containing the chain.. *chain is a pointer to the chain to add a residue to. *name is a pointer to a string containing the name of the residue. **residue is a pointer to a pointer to the newly created residue. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_chain_residue_add(tng_trajectory_t tng_data, tng_chain_t chain, const char *name, tng_residue_t *residue); /* Set the name of a residue. tng_data is the trajectory data container containing the residue.due. *residue is a pointer to the residue to rename. *new_name is a string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_residue_name_set(tng_trajectory_t tng_data, tng_residue_t residue, const char *new_name); /* Add an atom to a residue. *tng_data is a pointer to the trajectory containing the residue. *residue is a pointer to the residue to add an atom to. *atom_name is a pointer to a string containing the name of the atom. *atom_type is a pointer to a string containing the atom type of the atom. **atom is a pointer to a pointer to the newly created atom. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_residue_atom_add(tng_trajectory_t tng_data, tng_residue_t residue, const char *atom_name, const char *atom_type, tng_atom_t *atom); /* Set the name of an atom. tng_data is the trajectory data container containing the atom.. *atom is a pointer to the atom to rename. *new_name is a string containing the wanted name. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_atom_name_set(tng_trajectory_t tng_data, tng_atom_t atom, const char *new_name); /* Set the atom type of an atom. tng_data is the trajectory data container containing the atom.. *atom is a pointer to the atom to change. *new_name is a string containing the atom type. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, tng_atom_t atom, const char *new_type); /* Read the header blocks from the input_file of tng_data. The trajectory blocks must be read separately and iteratively in chunks to fit in memory. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. If hash_mode == TNG_USE_HASH the written md5 hash in the file will be compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_file_headers_read(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); /* Write the header blocks to the output_file of tng_data. The trajectory blocks must be written separately and iteratively in chunks to fit in memory. tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); /* Read one (the next) block (of any kind) from the input_file of tng_data. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. *block_data is a pointer to the struct which will be populated with the data. If block_data->input_file_pos > 0 it is the position from where the reading starts otherwise it starts from the current position. If hash_mode == TNG_USE_HASH the written md5 hash in the file will be compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_block_read_next(tng_trajectory_t tng_data, struct tng_gen_block *block_data, const tng_hash_mode hash_mode); /* Read one (the next) frame set, including toc, mapping and related data blocks from the input_file of tng_data. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. If hash_mode == TNG_USE_HASH the written md5 hash in the file will be compared to the md5 hash of the read contents to ensure valid data. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_read_next(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); /* Write one frame set, including toc, mapping and related data blocks to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. If hash_mode == TNG_USE_HASH an md5 hash for each block will be generated. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, const tng_hash_mode hash_mode); tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames); tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, 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); /* Read one trajectory block from the input_file of tng_data. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. block_id is the ID of the block to read. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_traj_block_read(tng_trajectory_t tng_data, int64_t block_id); /* Write one trajectory block to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. block_id is the ID of the block to write. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_traj_block_write(tng_trajectory_t tng_data, int64_t block_id); /* Read a requested frame set. tng_data is a trajectory data container. tng_data->current_trajectory_frame_set will be the read frame set. frame_set_nr is the number of the frame set to return (starting from 0). Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_set_read_nr(tng_trajectory_t tng_data, int64_t frame_set_nr); /* Read a number of consecutive trajectory frames from the input_file of tng_data. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. start_frame_nr is the index number of the first frame to read. end_frame_nr is the index number of the last frame to read. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); /* Write a number of consecutive trajectory frames to the output_file of tng_data. tng_data is a trajectory data container. tng_data->output_file_path specifies which file to write to. If the file (output_file) is not open it will be opened. start_frame_nr is the index number of the first frame to write. end_frame_nr is the index number of the last frame to write. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); /* Retrieve non-particle data from the last read frame set. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. block_id is the id number of the data block to read. ***values is a pointer to a 2-dimensional array (memory unallocated), which will be filled with data. The array will be sized (n_frames * n_values_per_frame). Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_data_get(tng_trajectory_t tng_data, int64_t block_id, union data_values ***values); /* Read and retrieve non-particle data, in a specific interval, from the trajectory. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. block_id is the id number of the data block to read. start_frame_nr is the index number of the first frame to read. end_frame_nr is the index number of the last frame to read. ***values is a pointer to a 2-dimensional array (memory unallocated), which will be filled with data. The array will be sized (n_frames * n_values_per_frame). Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, int64_t block_id, int64_t start_frame_nr, int64_t end_frame_nr, union data_values ***values); /* Retrieve particle data, from the last read frame set. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. block_id is the id number of the particle data block to read. ****values is a pointer to a 3-dimensional array (memory unallocated), which will be filled with data. The array will be sized (n_frames * n_particles * n_values_per_frame). Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, int64_t block_id, union data_values ****values); /* Read and retrieve particle data, in a specific interval, from the trajectory. tng_data is a trajectory data container. tng_data->input_file_path specifies which file to read from. If the file (input_file) is not open it will be opened. block_id is the id number of the particle data block to read. start_frame_nr is the index number of the first frame to read. end_frame_nr is the index number of the last frame to read. first_particle_number is the number of the first particle, for which to retrive data. last_particle_number is the number of the last particle, for which to retrieve data. ****values is a pointer to a 3-dimensional array (memory unallocated), which will be filled with data. The array will be sized (n_frames * n_particles * n_values_per_frame). Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, int64_t block_id, int64_t start_frame_nr, int64_t end_frame_nr, int64_t first_particle_number, int64_t last_particle_number, union data_values ****values); /* Get the date and time of initial file creation in ISO format (string). tng_data is a trajectory data container. *time is a pointer to the string in which the date will be stored. Memory must be reserved beforehand. Returns TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status tng_time_get_str(tng_trajectory_t tng_data, char *time); #ifdef __cplusplus } /* end extern "C" */ #endif #endif /* _TNGIO_H */