diff options
Diffstat (limited to 'src/lib/tng_io.h')
| -rw-r--r-- | src/lib/tng_io.h | 61 |
1 files changed, 52 insertions, 9 deletions
diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index ed9740e..baeea4c 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -47,7 +47,19 @@ * * @section examples_sec Examples * - * @subsection C + * @subsection tng_subsec TNG files + * + * The build directory contains an example_files directory, which in turn + * contains a very short example of a TNG file containing a few water molecules, + * a box shape description and positions in 10 frames. + * + * It is also possible to run the bin/md_openmp testing program, which will + * save MD simulations output to a new file (saved in the example_files + * directory). + * + * These files can be read using the bin/tng_io_read_pos testing program. + * + * @subsection c_subsec C * * \code * // These includes must be fixed in order to compile the example. @@ -151,6 +163,14 @@ * } * * \endcode + * + * @subsection fortran_subsec Fortran + * + * The TNG library can be used from Fortran. It requires cray pointers, which + * are not part of the Fortran 77 standard, but available in most compilers. + * + * To compile the fortran example -DBUILD_FORTRAN=ON needs to be specified when + * running cmake. * */ @@ -167,6 +187,7 @@ /** Flag to indicate particle dependent data. */ #define TNG_PARTICLE_DEPENDENT 1 + /** Flag to indicate frame dependent data. */ #define TNG_FRAME_DEPENDENT 2 @@ -190,52 +211,62 @@ __typeof__ (b) _b = (b); \ _a > _b ? _a : _b; }) - +/** Flag to specify the endianness of 32 bit values of the current architecture. + * Output is always converted to big endian */ typedef enum {TNG_BIG_ENDIAN_32, TNG_LITTLE_ENDIAN_32, TNG_BYTE_PAIR_SWAP_32} tng_endianness_32; +/** Flag to specify the endianness of 64 bit values of the current architecture. + * Output is always converted to big endian */ 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; - +/** Compression mode is specified in each data block */ typedef enum {TNG_UNCOMPRESSED, TNG_XTC_COMPRESSION, TNG_TNG_COMPRESSION} tng_compression; +/** Non trajectory blocks come before the first frame set block */ typedef enum {TNG_NON_TRAJECTORY_BLOCK, TNG_TRAJECTORY_BLOCK} tng_block_type; +/** Block IDs of standard non trajectory blocks. */ typedef enum {TNG_GENERAL_INFO, TNG_MOLECULES, TNG_TRAJECTORY_FRAME_SET, TNG_PARTICLE_MAPPING} tng_non_trajectory_block_ids; +/** Block IDs of standard trajectory blocks. Box shape can be either a + * trajectory block or a non-trajectory block */ typedef enum {TNG_TRAJ_BOX_SHAPE = 10000, TNG_TRAJ_POSITIONS, TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES} tng_trajectory_block_ids; - +/** Flag to specify if a data block contains data related to particles or not.*/ 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; +/** Flag to specify if the number of atoms change throughout the trajectory or + * if it is constant. */ typedef enum {TNG_CONSTANT_N_ATOMS, TNG_VARIABLE_N_ATOMS} tng_variable_n_atoms_flag; +/** Return values of API functions */ typedef enum {TNG_SUCCESS, TNG_FAILURE, TNG_CRITICAL} tng_function_status; +/** If tng_hash_mode == TNG_USE_HASH md5 hashes will be written to output files + * and when reading a file the md5 hashes of the contents will be compared to + * those in the file (for each block) in order to ensure data integrity */ typedef enum {TNG_SKIP_HASH, TNG_USE_HASH} tng_hash_mode; +/** Possible formats of data block contents */ typedef enum {TNG_CHAR_DATA, TNG_INT_DATA, TNG_FLOAT_DATA, @@ -254,16 +285,28 @@ struct tng_trajectory_frame_set; struct tng_particle_data; struct tng_non_particle_data; +/** A pointer to the main trajectory data storage. */ typedef struct tng_trajectory *tng_trajectory_t; +/** A pointer to a molecule description. */ typedef struct tng_molecule *tng_molecule_t; +/** A pointer to a molecular chain description. */ typedef struct tng_chain *tng_chain_t; +/** A pointer to a molecular residue description. */ typedef struct tng_residue *tng_residue_t; +/** A pointer to a molecular atom description. */ typedef struct tng_atom *tng_atom_t; +/** A pointer to a bond between two atoms. */ typedef struct tng_bond *tng_bond_t; +/** A pointer to a structure containing data common to all trajectory blocks, + * such as header and contents. */ typedef struct tng_gen_block *tng_gen_block_t; +/** A pointer to particle mapping information. */ typedef struct tng_particle_mapping *tng_particle_mapping_t; +/** A pointer to a structure containing frame set information. */ typedef struct tng_trajectory_frame_set *tng_trajectory_frame_set_t; +/** A pointer to a particle data container. */ typedef struct tng_particle_data *tng_particle_data_t; +/** A pointer to a non-particle data container. */ typedef struct tng_non_particle_data *tng_non_particle_data_t; /** Data can be either double, float, int or a string */ |