diff options
Diffstat (limited to 'src/lib/tng_io.h')
| -rw-r--r-- | src/lib/tng_io.h | 476 |
1 files changed, 130 insertions, 346 deletions
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 2ad8f23..80d93a4 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -129,8 +129,6 @@ typedef enum {TNG_CONSTANT_N_ATOMS, TNG_VARIABLE_N_ATOMS} 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, @@ -139,7 +137,18 @@ typedef enum {TNG_CHAR_DATA, TNG_DOUBLE_DATA} tng_data_type; - +struct tng_trajectory; +struct tng_molecule; +struct tng_chain; +struct tng_residue; +struct tng_atom; +struct tng_bond; +struct tng_gen_block; +struct tng_frame_set_toc; +struct tng_particle_mapping; +struct tng_trajectory_frame_set; +struct tng_particle_data; +struct tng_non_particle_data; typedef struct tng_trajectory *tng_trajectory_t; typedef struct tng_molecule *tng_molecule_t; @@ -147,164 +156,12 @@ 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 { - /** One of the atoms of the bond */ - int64_t from_atom_id; - /** The other atom of the bond */ - int64_t to_atom_id; -}; - -struct tng_atom { - /** The residue containing this atom */ - tng_residue_t residue; - /** A unique (per molecule) ID number of the atom */ - int64_t id; - /** The atom_type (depending on the forcefield) */ - char *atom_type; - /** The name of the atom */ - char *name; -}; - -struct tng_residue { - /** The chain containing this residue */ - tng_chain_t chain; - /** A unique (per chain) ID number of the residue */ - int64_t id; - /** The name of the residue */ - char *name; - /** The number of atoms in the residue */ - int64_t n_atoms; - /** A list of atoms in the residue */ - tng_atom_t atoms; -}; - -struct tng_chain { - /** The molecule containing this chain */ - tng_molecule_t molecule; - /** A unique (per molecule) ID number of the chain */ - int64_t id; - /** The name of the chain */ - char *name; - /** The number of residues in the chain */ - int64_t n_residues; - /** A list of residues in the chain */ - tng_residue_t residues; -}; - -struct tng_molecule { - /** A unique ID number of the molecule */ - int64_t id; - /** Quaternary structure of the molecule. - * 1 => monomeric - * 2 => dimeric - * 3 => trimeric - * etc */ - int64_t quaternary_str; - /** The number of chains in the molecule */ - int64_t n_chains; - /** The number of residues in the molecule */ - int64_t n_residues; - /** The number of atoms in the molecule */ - int64_t n_atoms; - /** The number of bonds in the molecule. If the bonds are not specified this - * value can be 0. */ - int64_t n_bonds; - /** The name of the molecule */ - char *name; - /** A list of chains in the molecule */ - tng_chain_t chains; - /** A list of residues in the molecule */ - tng_residue_t residues; - /** A list of the atoms in the molecule */ - tng_atom_t atoms; - /** A list of the bonds in the molecule */ - tng_bond_t bonds; -}; - -struct tng_gen_block { - /** The size of the block header in bytes */ - int64_t header_contents_size; - /** The size of the block contents in bytes */ - int64_t block_contents_size; - /** The ID of the block to determine its type */ - int64_t id; - /** The MD5 hash of the block to verify integrity */ - char hash[TNG_HASH_LEN]; - /** The name of the block */ - char *name; - /** The library version used to write the block */ - int64_t block_version; - /** The full block header contents */ - char *header_contents; - /** The full block contents */ - char *block_contents; -}; - -struct tng_frame_set_toc { - /** The number of blocks listed in this table of contents */ - int64_t n_blocks; - /** A list of block names */ - char **block_names; -}; - -struct tng_particle_mapping { - /** The index number of the first particle in this mapping block */ - int64_t num_first_particle; - /** The number of particles list in this mapping block */ - int64_t n_particles; - /** the mapping of index numbers to the real particle numbers in the - * trajectory. real_particle_numbers[0] is the real particle number - * (as it is numbered in the molecular system) of the first particle - * in the data blocks covered by this particle mapping block */ - int64_t *real_particle_numbers; -}; - -struct tng_trajectory_frame_set { - /** The table of contents of this frame set */ - struct tng_frame_set_toc contents; - /** The number of different particle mapping blocks present. */ - int64_t n_mapping_blocks; - /** The atom mappings of this frame set */ - struct tng_particle_mapping *mappings; - /** The first frame of this frame set */ - int64_t first_frame; - /** The number of frames in this frame set */ - int64_t n_frames; - /** A list of the number of each molecule type - only used when using - * variable number of atoms */ - int64_t *molecule_cnt_list; - /** The number of particles/atoms - only used when using variable number - * of atoms */ - int64_t n_particles; - /** The file position of the next frame set */ - int64_t next_frame_set_file_pos; - /** The file position of the previous frame set */ - int64_t prev_frame_set_file_pos; - /** The file position of the frame set one long stride step ahead */ - int64_t medium_stride_next_frame_set_file_pos; - /** The file position of the frame set one long stride step behind */ - int64_t medium_stride_prev_frame_set_file_pos; - /** The file position of the frame set one long stride step ahead */ - int64_t long_stride_next_frame_set_file_pos; - /** The file position of the frame set one long stride step behind */ - int64_t long_stride_prev_frame_set_file_pos; - - /* The data blocks in a frame set are trajectory data blocks */ - /** The number of trajectory data blocks of particle dependent data */ - int n_particle_data_blocks; - /** A list of data blocks containing particle dependent data */ - struct tng_particle_data *tr_particle_data; - /** The number of trajectory data blocks independent of particles */ - int n_data_blocks; - /** A list of data blocks containing particle indepdendent data */ - struct tng_data *tr_data; -}; +typedef struct tng_gen_block *tng_gen_block_t; +typedef struct tng_frame_set_toc *tng_frame_set_toc_t; +typedef struct tng_particle_mapping *tng_particle_mapping_t; +typedef struct tng_trajectory_frame_set *tng_trajectory_frame_set_t; +typedef struct tng_particle_data *tng_particle_data_t; +typedef struct tng_non_particle_data *tng_non_particle_data_t; /** Data can be either double, float, int or a string */ union data_values { @@ -314,182 +171,32 @@ union data_values { char *c; }; -/* FIXME: Should there be a pointer to a tng_gen_block from each data block? */ -struct tng_particle_data { - /** The block ID of the data block containing this particle data. - * This is used to determine the kind of data that is stored */ - int64_t block_id; - /** The name of the data block. This is used to determine the kind of - * data that is stored */ - char *block_name; - /** The type of data stored. */ - tng_data_type datatype; - /** The first frame number of the first data value */ - int64_t first_frame_with_data; - /** The number of frames in this frame set */ - int64_t n_frames; - /** The number of values stored per frame */ - int64_t n_values_per_frame; - /** The number of frames between each data point - e.g. when - * storing sparse data. */ - int64_t stride_length; - /** ID of the CODEC used for compression 0 == no compression. */ - int64_t codec_id; - /** The multiplier used for getting integer values for compression */ - double compression_multiplier; - /** A 3-dimensional array of values, sized - * n_frames * n_particles * n_values_per_frame */ - union data_values ***values; -}; - -struct tng_data { - /** The ID of the data block */ - int64_t block_id; - /** The name of the data block. This is used to determine the kind of - * data that is stored */ - char *block_name; - /** The type of data stored. */ - tng_data_type datatype; - /** The first frame number of the first data value */ - int64_t first_frame_with_data; - /** The number of frames in this data block */ - int64_t n_frames; - /** The number of values stored per frame */ - int64_t n_values_per_frame; - /** The number of frames between each data value, e.g. if storing data - * that is not saved every frame. */ - int64_t stride_length; - /** ID of the CODEC used for compression. 0 == no compression. */ - int64_t codec_id; - /** Compressed data is stored as integers. This compression multiplier is - * the multiplication factor to convert from integer to float/double */ - double compression_multiplier; - /** A 2-dimensional array of values, sized n_frames * n_values_per_frame */ - union data_values **values; -}; - - -struct tng_trajectory { - /** The path of the input trajectory file */ - char *input_file_path; - /** A handle to the input file */ - FILE *input_file; - /** The reading position of the file */ - long int input_file_pos; - /** The length of the input file */ - long int input_file_len; - /** The path of the output trajectory file */ - char *output_file_path; - /** A handle to the output file */ - FILE *output_file; - /** The writing position of the file */ - long int output_file_pos; - /** The endianness of 32 bit values of the current computer */ - tng_endianness_32 endianness_32; - /** The endianness of 64 bit values of the current computer */ - tng_endianness_64 endianness_64; - - /** The name of the program producing this trajectory */ - char *first_program_name; - /** The forcefield used in the simulations */ - char *forcefield_name; - /** The name of the user running the simulations */ - char *first_user_name; - /** The name of the computer on which the simulations were performed */ - char *first_computer_name; - /** The PGP signature of the user creating the file. */ - char *first_pgp_signature; - /** The name of the program used when making last modifications to the - * file */ - char *last_program_name; - /** The name of the user making the last modifications to the file */ - char *last_user_name; - /** The name of the computer on which the last modifications were made */ - char *last_computer_name; - /** The PGP signature of the user making the last modifications to the - * file. */ - char *last_pgp_signature; - /** The time (n seconds since 1970) when the file was created */ - int64_t time; - - /** A flag indicating if the number of atoms can vary throughout the - * simulation, e.g. using a grand canonical ensemble */ - char var_num_atoms_flag; - /** 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 frame_set_n_frames; - /** The number of frame sets in a medium stride step */ - int64_t medium_stride_length; - /** The number of frame sets in a long stride step */ - int64_t long_stride_length; - - /** The number of different kinds of molecules in the trajectory */ - int64_t n_molecules; - /** A list of molecules in the trajectory */ - tng_molecule_t molecules; - /** A list of the count of each molecule - if using variable number of - * particles this will be specified in each frame set */ - int64_t *molecule_cnt_list; - /** The total number of particles/atoms. If using variable number of - * particles this will be specified in each frame set */ - int64_t n_particles; - - /** The pos in the src file of the first frame set */ - int64_t first_trajectory_frame_set_input_file_pos; - /** The pos in the dest file of the first frame set */ - int64_t first_trajectory_frame_set_output_file_pos; - /** The pos in the src file of the last frame set */ - int64_t last_trajectory_frame_set_input_file_pos; - /** The pos in the dest file of the last frame set */ - int64_t last_trajectory_frame_set_output_file_pos; - /** The currently active frame set */ - struct tng_trajectory_frame_set current_trajectory_frame_set; - /** The pos in the src file of the current frame set */ - long int current_trajectory_frame_set_input_file_pos; - /** The pos in the dest file of the current frame set */ - long int current_trajectory_frame_set_output_file_pos; - /** The number of frame sets in the trajectory */ - int64_t n_trajectory_frame_sets; - - /** The number of trajectory blocks in the file */ - int64_t n_trajectory_blocks; - /** The number of non-trajectory blocks in the file */ - int64_t n_non_trajectory_blocks; - /** A list of non-trajectory blocks */ - struct tng_gen_block non_trajectory_blocks[32]; - - /* These data blocks are non-trajectory data blocks */ - /** The number of non-frame dependent particle dependent data blocks */ - int n_particle_data_blocks; - /** A list of data blocks containing particle dependent data */ - struct tng_particle_data *non_tr_particle_data; - - /** The number of frame and particle independent data blocks */ - int n_data_blocks; - /** A list of frame and particle indepdendent data blocks */ - struct tng_data *non_tr_data; -}; +#ifdef __cplusplus +extern "C" +{ +#endif /** * @brief Setup a trajectory data container. - * @param tng_data pre-allocated memory to initialise as a trajectory. + * @param tng_data_p a pointer to memory to initialise as a trajectory. + * @details Memory is allocated during initialisation. * @return 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); +tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p); /** * @brief Clean up a trajectory data container. - * @param tng_data the trajectory data to destroy. - * @details All allocated memory in the data structure is freed, but not the memory - * of tng_data itself. + * @param tng_data_p a pointer to the trajectory data to destroy. + * @details All allocated memory in the data structure is freed, as well as + * tng_data_p itself. * @return 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); +tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p); /** * @brief Set the name of the input file. @@ -642,52 +349,123 @@ tng_function_status tng_long_stride_length_set(tng_trajectory_t tng_data, int64_t len); /** - * @brief Setup a molecule container. - * @param molecule is the molecule to initialise. Memory must be preallocated. + * @brief Get the reading position of the input file. + * @param tng_data is the trajectory from which to get the position. + * @param pos is pointing to a value set to the reading position. * @return 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); +tng_function_status tng_input_file_pos_get(tng_trajectory_t tng_data, + int64_t *pos); /** - * @brief Clean up a molecule container. - * @param molecule is the molecule to destroy. - * @details All allocated memory in the data structure is freed, but not the - * memory of molecule itself. + * @brief Get the writing position of the output file. + * @param tng_data is the trajectory from which to get the position. + * @param pos is pointing to a value set to the writing position. * @return 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); +tng_function_status tng_output_file_pos_get(tng_trajectory_t tng_data, + int64_t *pos); /** - * @brief Setup a data block. - * @param block is a pointer to pre-allocated memory. + * @brief Get the length of the input file. + * @param tng_data is the trajectory from which to get the input file length. + * @param len is pointing to a value set to the file length. * @return 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); +tng_function_status tng_input_file_len_get(tng_trajectory_t tng_data, + int64_t *len); /** - * @brief Clean up a data block. - * @param block is a pointer to pre-allocated memory. - * @details All allocated memory in the data structure is freed, but not the - * memory of block itself. + * @brief Get the current number of particles. + * @param tng_data is the trajectory from which to get the number of particles. + * @param n is pointing to a value set to the number of particles. + * @details If variable number of particles are used this function will return + * the number of particles in the current frame set. * @return 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); +tng_function_status tng_num_particles_get(tng_trajectory_t tng_data, + int64_t *n); /** - * @brief Set the name of a data block. - * @param tng_data is the trajectory data container containing the block.. - * @param block is a pointer to the block to rename. - * @param new_name is a string containing the wanted name. + * @brief Get the current total number of molecules. + * @param tng_data is the trajectory from which to get the number of molecules. + * @param n is pointing to a value set to the number of molecules. + * @details If variable number of particles are used this function will return + * the total number of molecules in the current frame set. * @return 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); +tng_function_status tng_num_molecules_get(tng_trajectory_t tng_data, + int64_t *n); + +/** + * @brief Get the number of frames per frame set. + * @param tng_data is the trajectory from which to get the number of frames + * per frame set. + * @param n is pointing to a value set to the number of frames per frame set. + * @return 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_num_frames_per_frame_set_get(tng_trajectory_t tng_data, + int64_t *n); + +/** + * @brief Get the current trajectory frame set. + * @param tng_data is the trajectory from which to get the frame set. + * @param frame_set is pointing to the memory position of the frame set. + * @return 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_current_frame_set_get + (tng_trajectory_t tng_data, + tng_trajectory_frame_set_t frame_set); + +/** + * @brief Get the file position of the next frame set in the input file. + * @param frame_set is the frame set of which to get the position of the + * following frame set. + * @param pos is pointing to a value set to the file position. + * @return 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_next_frame_set_file_pos_get + (tng_trajectory_frame_set_t frame_set, + int64_t *pos); + +/** + * @brief Get the file position of the previous frame set in the input file. + * @param frame_set is the frame set of which to get the position of the + * previous frame set. + * @param pos is pointing to a value set to the file position. + * @return 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_prev_frame_set_file_pos_get + (tng_trajectory_frame_set_t frame_set, + int64_t *pos); + +/** + * @brief Setup a molecule container. + * @param molecule is the molecule to initialise. Memory must be preallocated. + * @return 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); + +/** + * @brief Clean up a molecule container. + * @param molecule is the molecule to destroy. + * @details All allocated memory in the data structure is freed, but not the + * memory of molecule itself. + * @return 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); + /** * @brief Add a molecule to the trajectory. @@ -905,7 +683,7 @@ tng_function_status tng_file_headers_write(tng_trajectory_t tng_data, * 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, + tng_gen_block_t block_data, const tng_hash_mode hash_mode); @@ -1034,6 +812,9 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, * opened. * @param start_frame_nr is the index number of the first frame to read. * @param end_frame_nr is the index number of the last frame to read. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ @@ -1051,6 +832,9 @@ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, * opened. * @param start_frame_nr is the index number of the first frame to write. * @param end_frame_nr is the index number of the last frame to write. + * @param hash_mode is an option to decide whether to use the md5 hash or not. + * 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ |