diff options
| author | Magnus Lundborg <lundborg.magnus@gmail.com> | 2013-05-22 13:00:50 (GMT) |
|---|---|---|
| committer | Magnus Lundborg <lundborg.magnus@gmail.com> | 2013-05-22 13:00:50 (GMT) |
| commit | 0a4c5591fb33b862c867b1e31b3fd225e93fbf76 (patch) | |
| tree | aa1e4d3f481cf22379136edd24e66696003f8395 | |
| parent | 98900c813d6b037a3931c60836a1df0405e1d6c5 (diff) | |
New functions added (mainly utility functions).
New functions to simplify the work flow added. Not everything
is fully tested yet. More commits to follow.
| -rw-r--r-- | include/tng_io.h | 808 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 1798 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 18 |
3 files changed, 1716 insertions, 908 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index f2ae1c9..57ae8a4 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -499,90 +499,6 @@ extern "C" { #endif -tng_function_status tng_util_trajectory_open(const char *filename, - const char mode, - tng_trajectory_t *tng_data_p); - -tng_function_status tng_util_trajectory_close(tng_trajectory_t *tng_data_p); - -tng_function_status tng_util_trajectory_molecules_get(tng_trajectory_t tng_data, - int64_t *n_mols, - int64_t *molecule_cnt_list, - tng_molecule_t *mols); - -tng_function_status tng_util_trajectory_molecule_add(tng_trajectory_t tng_data, - const char *name, - const int64_t cnt, - tng_molecule_t *mol); - -tng_function_status tng_util_molecule_particles_get(tng_trajectory_t tng_data, - const tng_molecule_t mol, - int64_t *n_particles, - char ***names, - char ***types, - char ***res_names, - int64_t **res_ids, - char ***chain_names, - int64_t **chain_ids); - -tng_function_status tng_util_molecule_particles_set(tng_trajectory_t tng_data, - tng_molecule_t mol, - const int64_t n_particles, - const char **names, - const char **types, - const char **res_names, - const int64_t *res_ids, - const char **chain_names, - const int64_t *chain_ids); - -tng_function_status tng_util_pos_read(tng_trajectory_t tng_data, - float *positions); - -tng_function_status tng_util_vel_read(tng_trajectory_t tng_data, - float *velocities); - -tng_function_status tng_util_force_read(tng_trajectory_t tng_data, - float *forces); - -tng_function_status tng_util_box_shape_read(tng_trajectory_t tng_data, - float *box_shape); - -tng_function_status tng_util_pos_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *positions); - -tng_function_status tng_util_vel_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *velocities); - -tng_function_status tng_util_force_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *forces); - -tng_function_status tng_util_box_shape_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *box_shape); - -tng_function_status tng_util_pos_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *positions); - -tng_function_status tng_util_vel_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *velocities); - -tng_function_status tng_util_force_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *forces); - -tng_function_status tng_util_box_shape_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *box_shape); - /** * @brief Setup a trajectory data container. @@ -591,7 +507,8 @@ tng_function_status tng_util_box_shape_write(tng_trajectory_t tng_data, * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_data_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_init + (tng_trajectory_t *tng_data_p); /** * @brief Clean up a trajectory data container. @@ -600,7 +517,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_ * tng_data_p itself. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *tng_data_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy + (tng_trajectory_t *tng_data_p); /** * @brief Copy a trajectory data container (dest is setup as well). @@ -614,8 +532,8 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajectory_t src, - tng_trajectory_t *dest_p); +tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src + (tng_trajectory_t src, tng_trajectory_t *dest_p); /** * @brief Get the name of the input file. @@ -627,8 +545,9 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_input_file_get + (const tng_trajectory_t tng_data, + char *file_name, const int max_len); /** * @brief Set the name of the input file. @@ -637,8 +556,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_get(const tng_trajectory_t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_data, - const char *file_name); +tng_function_status DECLSPECDLLEXPORT tng_input_file_set + (tng_trajectory_t tng_data, + const char *file_name); /** * @brief Get the name of the output file. @@ -650,8 +570,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_set(tng_trajectory_t tng_da * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_output_file_get(const tng_trajectory_t tng_data, - char *file_name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_output_file_get + (const tng_trajectory_t tng_data, + char *file_name, const int max_len); /** * @brief Set the name of the output file. @@ -660,8 +581,9 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_get(const tng_trajectory_t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_output_file_set(tng_trajectory_t tng_data, - const char *file_name); +tng_function_status DECLSPECDLLEXPORT tng_output_file_set + (tng_trajectory_t tng_data, + const char *file_name); /** * @brief Get the endianness of the output file. @@ -698,8 +620,9 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the program used when creating the trajectory. @@ -708,8 +631,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get(const tng_traje * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the program used when last modifying the trajectory. @@ -721,8 +645,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set(tng_trajectory_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the program used when last modifying the trajectory. @@ -731,8 +656,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get(const tng_trajec * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the user who created the trajectory. @@ -744,8 +670,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set(tng_trajectory_t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the user who created the trajectory. @@ -754,8 +681,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the user who last modified the trajectory. @@ -767,8 +695,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the user who last modified the trajectory. @@ -777,8 +706,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get(const tng_trajector * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the computer used when creating the trajectory. @@ -790,8 +720,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the computer used when creating the trajectory. @@ -800,8 +731,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get(const tng_traj * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the name of the computer used when last modifying the trajectory. @@ -813,8 +745,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set(tng_trajectory * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the computer used when last modifying the trajectory. @@ -823,8 +756,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get(const tng_traje * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the pgp_signature of the user creating the trajectory. @@ -836,8 +770,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set(tng_trajectory_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_first_signature_get(const tng_trajectory_t tng_data, - char *signature, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_first_signature_get + (const tng_trajectory_t tng_data, + char *signature, const int max_len); /** * @brief Set the pgp_signature of the user creating the trajectory. @@ -846,8 +781,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_first_signature_set(tng_trajectory_t tng_data, - const char *signature); +tng_function_status DECLSPECDLLEXPORT tng_first_signature_set + (tng_trajectory_t tng_data, + const char *signature); /** * @brief Get the pgp_signature of the user last modifying the trajectory. @@ -859,8 +795,9 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_set(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_last_signature_get(const tng_trajectory_t tng_data, - char *signature, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_last_signature_get + (const tng_trajectory_t tng_data, + char *signature, const int max_len); /** * @brief Set the pgp_signature of the user last modifying the trajectory. @@ -869,8 +806,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_get(const tng_trajector * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_last_signature_set(tng_trajectory_t tng_data, - const char *signature); +tng_function_status DECLSPECDLLEXPORT tng_last_signature_set + (tng_trajectory_t tng_data, + const char *signature); /** * @brief Get the name of the forcefield used in the trajectory. @@ -882,8 +820,9 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_set(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ -tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get(const tng_trajectory_t tng_data, - char *name, const int max_len); +tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get + (const tng_trajectory_t tng_data, + char *name, const int max_len); /** * @brief Set the name of the forcefield used in the trajectory. @@ -892,8 +831,9 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get(const tng_trajecto * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set(tng_trajectory_t tng_data, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set + (tng_trajectory_t tng_data, + const char *new_name); /** * @brief Get the medium stride length of the trajectory. @@ -901,8 +841,9 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set(tng_trajectory_t t * @param len is pointing to a value set to the stride length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Set the medium stride length of the trajectory. @@ -911,8 +852,9 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get(const tng_tra * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ -tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set(tng_trajectory_t tng_data, - const int64_t len); +tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set + (tng_trajectory_t tng_data, + const int64_t len); /** * @brief Get the long stride length of the trajectory. @@ -920,8 +862,9 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set(tng_trajector * @param len is pointing to a value set to the stride length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Set the long stride length of the trajectory. @@ -930,8 +873,9 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get(const tng_traje * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ -tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set(tng_trajectory_t tng_data, - const int64_t len); +tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set + (tng_trajectory_t tng_data, + const int64_t len); /** * @brief Get the length of the input file. @@ -939,8 +883,9 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set(tng_trajectory_ * @param len is pointing to a value set to the file length. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get(const tng_trajectory_t tng_data, - int64_t *len); +tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get + (const tng_trajectory_t tng_data, + int64_t *len); /** * @brief Get the number of frames in the trajectory @@ -949,8 +894,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get(const tng_trajector * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (could not find last frame set). */ -tng_function_status DECLSPECDLLEXPORT tng_num_frames_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_frames_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the current number of particles. @@ -960,8 +906,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get(const tng_trajectory_t * the number of particles in the current frame set. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_num_particles_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_particles_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the current total number of molecules. @@ -971,8 +918,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_particles_get(const tng_trajectory * the total number of molecules in the current frame set. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get(const tng_trajectory_t tng_data, - int64_t *n); +tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get + (const tng_trajectory_t tng_data, + int64_t *n); /** * @brief Get the number of frames per frame set. @@ -1031,8 +979,9 @@ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get * @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 DECLSPECDLLEXPORT tng_frame_set_nr_find(tng_trajectory_t tng_data, - const int64_t nr); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find + (tng_trajectory_t tng_data, + const int64_t nr); /** * @brief Find the frame set containing a specific frame. @@ -1043,8 +992,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find(tng_trajectory_t tng * @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 DECLSPECDLLEXPORT tng_frame_set_of_frame_find(tng_trajectory_t tng_data, - const int64_t frame); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find + (tng_trajectory_t tng_data, + const int64_t frame); /** * @brief Get the file position of the next frame set in the input file. @@ -1093,8 +1043,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_frame_range_get * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t tng_data, - tng_molecule_t molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_init + (const tng_trajectory_t tng_data, + tng_molecule_t molecule); /** * @brief Clean up a molecule container. @@ -1105,8 +1056,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_t tng_data, - tng_molecule_t molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy + (const tng_trajectory_t tng_data, + tng_molecule_t molecule); /** * @brief Add a molecule to the trajectory. @@ -1116,9 +1068,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_add(tng_trajectory_t tng_data, - const char *name, - tng_molecule_t *molecule); +tng_function_status DECLSPECDLLEXPORT tng_molecule_add + (tng_trajectory_t tng_data, + const char *name, + tng_molecule_t *molecule); /** * @brief Set the name of a molecule. @@ -1128,9 +1081,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add(tng_trajectory_t tng_data * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *new_name); /** * @brief Get the count of a molecule. @@ -1140,9 +1094,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set(tng_trajectory_t tng * @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 DECLSPECDLLEXPORT tng_molecule_cnt_get(tng_trajectory_t tng_data, - tng_molecule_t molecule, - int64_t *cnt); +tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + int64_t *cnt); /** * @brief Set the count of a molecule. @@ -1152,9 +1107,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get(tng_trajectory_t tng_ * @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 DECLSPECDLLEXPORT tng_molecule_cnt_set(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const int64_t cnt); +tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const int64_t cnt); /** * @brief Find a chain in a molecule. @@ -1170,11 +1126,12 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set(tng_trajectory_t tng_ * @details If name is an empty string and id is -1 the first chain will be * found. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *name, - int64_t id, - tng_chain_t *chain); +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *name, + int64_t id, + tng_chain_t *chain); /** * @brief Add a chain to a molecule. @@ -1185,10 +1142,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find(tng_trajectory_t t * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add(tng_trajectory_t tng_data, - tng_molecule_t molecule, - const char *name, - tng_chain_t *chain); +tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add + (tng_trajectory_t tng_data, + tng_molecule_t molecule, + const char *name, + tng_chain_t *chain); /** * @brief Set the name of a chain. @@ -1198,9 +1156,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_name_set(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_chain_name_set + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *new_name); /** * @brief Find a residue in a chain. @@ -1212,11 +1171,12 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set(tng_trajectory_t tng_da * residue is not found. * @details If name is an empty string the first residue will be found. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *name, - int64_t id, - tng_residue_t *residue); +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *name, + int64_t id, + tng_residue_t *residue); /** * @brief Add a residue to a chain. @@ -1227,10 +1187,11 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find(tng_trajectory_t tn * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add(tng_trajectory_t tng_data, - tng_chain_t chain, - const char *name, - tng_residue_t *residue); +tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add + (tng_trajectory_t tng_data, + tng_chain_t chain, + const char *name, + tng_residue_t *residue); /** * @brief Set the name of a residue. @@ -1240,9 +1201,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_data, - tng_residue_t residue, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_residue_name_set + (tng_trajectory_t tng_data, + tng_residue_t residue, + const char *new_name); /** * @brief Add an atom to a residue. @@ -1254,11 +1216,12 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT 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); +tng_function_status DECLSPECDLLEXPORT 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); /** * @brief Set the name of an atom. @@ -1268,9 +1231,10 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add(tng_trajectory_t tng_ * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_atom_name_set(tng_trajectory_t tng_data, - tng_atom_t atom, - const char *new_name); +tng_function_status DECLSPECDLLEXPORT tng_atom_name_set + (tng_trajectory_t tng_data, + tng_atom_t atom, + const char *new_name); /** * @brief Set the atom type of an atom. @@ -1280,9 +1244,10 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_set(tng_trajectory_t tng_dat * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_atom_type_set(tng_trajectory_t tng_data, - tng_atom_t atom, - const char *new_type); +tng_function_status DECLSPECDLLEXPORT tng_atom_type_set + (tng_trajectory_t tng_data, + tng_atom_t atom, + const char *new_type); /** * @brief Get the molecume name of real particle number (number in mol system). @@ -1403,8 +1368,9 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_file_headers_read(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_file_headers_read + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Write the header blocks to the output_file of tng_data. @@ -1419,8 +1385,9 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read(tng_trajectory_t tng * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ -tng_function_status DECLSPECDLLEXPORT tng_file_headers_write(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_file_headers_write + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Read one (the next) block (of any kind) from the input_file of tng_data. @@ -1438,9 +1405,10 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write(tng_trajectory_t tn * @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 DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_data, - tng_gen_block_t block_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_block_read_next + (tng_trajectory_t tng_data, + tng_gen_block_t block_data, + const tng_hash_mode hash_mode); /** * @brief Read one (the next) frame set, including mapping and related data blocks @@ -1455,8 +1423,9 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_d * @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 DECLSPECDLLEXPORT tng_frame_set_read_next(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Write one frame set, including mapping and related data blocks @@ -1470,8 +1439,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next(tng_trajectory_t t * @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 DECLSPECDLLEXPORT tng_frame_set_write(tng_trajectory_t tng_data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_write + (tng_trajectory_t tng_data, + const tng_hash_mode hash_mode); /** * @brief Create and initialise a frame set. @@ -1482,9 +1452,10 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_write(tng_trajectory_t tng_d * @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 DECLSPECDLLEXPORT tng_frame_set_new(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t n_frames); +tng_function_status DECLSPECDLLEXPORT tng_frame_set_new + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t n_frames); /** * @brief Add a non-particle dependent data block. @@ -1507,16 +1478,17 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new(tng_trajectory_t tng_dat * @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 DECLSPECDLLEXPORT tng_data_block_add(tng_trajectory_t tng_data, - const int64_t id, - const char *block_name, - const tng_data_type datatype, - const tng_block_type block_type_flag, - int64_t n_frames, - const int64_t n_values_per_frame, - int64_t stride_length, - const int64_t codec_id, - void *new_data); +tng_function_status DECLSPECDLLEXPORT tng_data_block_add + (tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const tng_data_type datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + int64_t stride_length, + const int64_t codec_id, + void *new_data); /** * @brief Add a particle dependent data block. @@ -1542,18 +1514,19 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add(tng_trajectory_t tng_da * @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 DECLSPECDLLEXPORT tng_particle_data_block_add(tng_trajectory_t tng_data, - const int64_t id, - const char *block_name, - const tng_data_type datatype, - const tng_block_type block_type_flag, - int64_t n_frames, - const int64_t n_values_per_frame, - int64_t stride_length, - const int64_t first_particle_number, - const int64_t n_particles, - const int64_t codec_id, - void *new_data); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add + (tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const tng_data_type datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + int64_t stride_length, + const int64_t first_particle_number, + const int64_t n_particles, + const int64_t codec_id, + void *new_data); /** * @brief Write data of one trajectory frame to the output_file of tng_data. @@ -1570,11 +1543,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add(tng_trajectory * @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 DECLSPECDLLEXPORT tng_frame_data_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const int64_t block_id, - const void *data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_data_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const int64_t block_id, + const void *data, + const tng_hash_mode hash_mode); /** * @brief Write particle data of one trajectory frame to the output_file of @@ -1595,13 +1569,14 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write(tng_trajectory_t tng_ * @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 DECLSPECDLLEXPORT tng_frame_particle_data_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const int64_t block_id, - const int64_t val_first_particle, - const int64_t val_n_particles, - const void *data, - const tng_hash_mode hash_mode); +tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const int64_t block_id, + const int64_t val_first_particle, + const int64_t val_n_particles, + const void *data, + const tng_hash_mode hash_mode); /** * @brief Free data of an array of values (2D). @@ -1612,11 +1587,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write(tng_trajecto * @param type is the data type of the data in the array (e.g. int/float/char). * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_data_values_free(const tng_trajectory_t tng_data, - union data_values **values, - const int64_t n_frames, - const int64_t n_values_per_frame, - const tng_data_type type); +tng_function_status DECLSPECDLLEXPORT tng_data_values_free + (const tng_trajectory_t tng_data, + union data_values **values, + const int64_t n_frames, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Free data of an array of values (3D). @@ -1628,12 +1604,13 @@ tng_function_status DECLSPECDLLEXPORT tng_data_values_free(const tng_trajectory_ * @param type is the data type of the data in the array (e.g. int/float/char). * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_trajectory_t tng_data, - union data_values ***values, - const int64_t n_frames, - const int64_t n_particles, - const int64_t n_values_per_frame, - const tng_data_type type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free + (const tng_trajectory_t tng_data, + union data_values ***values, + const int64_t n_frames, + const int64_t n_particles, + const int64_t n_values_per_frame, + const tng_data_type type); /** * @brief Retrieve non-particle data, from the last read frame set. @@ -1646,7 +1623,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_tr * (n_frames * n_values_per_frame). * Since ***values is allocated in this function it is the callers * responsibility to free the memory. - * @param n_frames is set to the number of particles in the returned data. This is + * @param n_frames is set to the number of frames in the returned data. This is * needed to properly reach and/or free the data afterwards. * @param n_values_per_frame is set to the number of values per frame in the data. * This is needed to properly reach and/or free the data afterwards. @@ -1655,11 +1632,11 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free(const tng_tr * has occurred or TNG_CRITICAL (2) if a major error has occured. */ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, - const int64_t block_id, - union data_values ***values, - int64_t *n_frames, - int64_t *n_values_per_frame, - tng_data_type *type); + const int64_t block_id, + union data_values ***values, + int64_t *n_frames, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Retrieve a vector (1D array) of non-particle data, from the last read frame set. @@ -1673,6 +1650,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_data, * responsibility to free the memory. * @param n_frames is set to the number of particles in the returned data. This is * needed to properly reach and/or free the data afterwards. + * @param stride_length is set to the stride length of the returned data. * @param n_values_per_frame is set to the number of values per frame in the data. * This is needed to properly reach and/or free the data afterwards. * @param type is set to the data type of the data in the array. @@ -1680,12 +1658,14 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_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. */ -tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, - const int64_t block_id, - void **values, - int64_t *n_frames, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_data_vector_get + (tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + int64_t *n_frames, + int64_t *stride_length, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Read and retrieve non-particle data, in a specific interval. @@ -1709,14 +1689,48 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_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. */ -tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng_data, - const int64_t block_id, - const int64_t start_frame_nr, - const int64_t end_frame_nr, - const tng_hash_mode hash_mode, - union data_values ***values, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_data_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type); + +/** + * @brief Read and retrieve a vector (1D array) of non-particle data, + * in a specific interval. + * @param 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. + * @param block_id is the id number of the particle data block to read. + * @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 md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be (n_frames * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) 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. + */ +tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Retrieve particle data, from the last read frame set. @@ -1732,7 +1746,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng * (n_frames * n_particles * n_values_per_frame). * Since ****values is allocated in this function it is the callers * responsibility to free the memory. - * @param n_frames is set to the number of particles in the returned data. This is + * @param n_frames is set to the number of frames in the returned data. This is * needed to properly reach and/or free the data afterwards. * @param n_particles is set to the number of particles in the returned data. This is * needed to properly reach and/or free the data afterwards. @@ -1742,13 +1756,50 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get(tng_trajectory_t tng * @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 DECLSPECDLLEXPORT tng_particle_data_get(tng_trajectory_t tng_data, - const int64_t block_id, - union data_values ****values, - int64_t *n_frames, - int64_t *n_particles, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_get + (tng_trajectory_t tng_data, + const int64_t block_id, + union data_values ****values, + int64_t *n_frames, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); + +/** + * @brief Retrieve a vector (1D array) of particle data, from the last read frame set. + * @details The particle dimension of the returned values array is translated + * to real particle numbering, i.e. the numbering of the actual molecular + * system. + * @param 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. + * @param block_id is the id number of the particle data block to read. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be + * (n_frames * n_particles * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_frames is set to the number of frames in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param stride_length is set to the stride length of the returned data. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) 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. + */ +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get + (tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + int64_t *n_frames, + int64_t *stride_length, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); /** * @brief Read and retrieve particle data, in a specific interval. @@ -1777,15 +1828,55 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get(tng_trajectory_t tng * @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 DECLSPECDLLEXPORT tng_particle_data_interval_get(tng_trajectory_t tng_data, - const int64_t block_id, - const int64_t start_frame_nr, - const int64_t end_frame_nr, - const tng_hash_mode hash_mode, - union data_values ****values, - int64_t *n_particles, - int64_t *n_values_per_frame, - tng_data_type *type); +tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ****values, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); +/** + * @brief Read and retrieve a vector (1D array) particle data, in a + * specific interval. + * @details The particle dimension of the returned values array is translated + * to real particle numbering, i.e. the numbering of the actual molecular + * system. + * @param 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. + * @param block_id is the id number of the particle data block to read. + * @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 md5 hash in the file will be + * compared to the md5 hash of the read contents to ensure valid data. + * @param values is a pointer to a 1-dimensional array (memory unallocated), which + * will be filled with data. The length of the array will be + * (n_frames * n_particles * n_values_per_frame). + * Since **values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. + * @param type is set to the data type of the data in the array. + * @details This does only work for numerical (int, float, double) 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. + */ +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + void **values, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type); /** @brief Get the date and time of initial file creation in ISO format (string). * @param tng_data is a trajectory data container. @@ -1793,8 +1884,123 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get(tng_traject must be reserved beforehand. * @return TNG_SUCCESS (0) if successful. */ -tng_function_status DECLSPECDLLEXPORT tng_time_get_str(const tng_trajectory_t tng_data, - char *time); +tng_function_status DECLSPECDLLEXPORT tng_time_get_str + (const tng_trajectory_t tng_data, + char *time); + + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open + (const char *filename, + const char mode, + tng_trajectory_t *tng_data_p); + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close + (tng_trajectory_t *tng_data_p); + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get + (tng_trajectory_t tng_data, + int64_t *n_mols, + int64_t *molecule_cnt_list, + tng_molecule_t *mols); + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add + (tng_trajectory_t tng_data, + const char *name, + const int64_t cnt, + tng_molecule_t *mol); + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get + (tng_trajectory_t tng_data, + const tng_molecule_t mol, + int64_t *n_particles, + char ***names, + char ***types, + char ***res_names, + int64_t **res_ids, + char ***chain_names, + int64_t **chain_ids); + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set + (tng_trajectory_t tng_data, + tng_molecule_t mol, + const int64_t n_particles, + const char **names, + const char **types, + const char **res_names, + const int64_t *res_ids, + const char **chain_names, + const int64_t *chain_ids); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read + (tng_trajectory_t tng_data, + float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read + (tng_trajectory_t tng_data, + float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read + (tng_trajectory_t tng_data, + float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read + (tng_trajectory_t tng_data, + float *box_shape); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *box_shape); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequence_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequence_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequence_set + (tng_trajectory_t tng_data, const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *positions); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *velocities); + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *forces); + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *box_shape); diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 410fb7c..4a76d25 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -145,7 +145,7 @@ struct tng_trajectory_frame_set { /** The number of frames in this frame set */ int64_t n_frames; /** The number of written frames in this frame set (used when writing one - * frame at a time. */ + * frame at a time). */ int64_t n_written_frames; /** A list of the number of each molecule type - only used when using @@ -364,217 +364,6 @@ struct tng_trajectory { #define TNG_SNPRINTF snprintf #endif -tng_function_status tng_util_trajectory_open(const char *filename, - const char mode, - tng_trajectory_t *tng_data_p) -{ - if(mode != 'r' && mode != 'w' && mode != 'a') - { - return(TNG_FAILURE); - } - - if(tng_trajectory_init(tng_data_p) != TNG_SUCCESS) - { - tng_trajectory_destroy(tng_data_p); - return(TNG_CRITICAL); - } - - if(mode == 'r' || mode == 'a') - { - tng_input_file_set(*tng_data_p, filename); - - // Read the file headers - tng_file_headers_read(*tng_data_p, TNG_USE_HASH); - } - - if(mode == 'w' || mode == 'a') - { - tng_output_file_set(*tng_data_p, filename); - } - - return(TNG_SUCCESS); -} - -tng_function_status tng_util_trajectory_close(tng_trajectory_t *tng_data_p) -{ - return(tng_trajectory_destroy(tng_data_p)); -} - -tng_function_status tng_util_trajectory_molecules_get(tng_trajectory_t tng_data, - int64_t *n_mols, - int64_t *molecule_cnt_list, - tng_molecule_t *mols) -{ - /* FIXME: This should return a copy of the molecules instead */ - *n_mols = tng_data->n_molecules; - - molecule_cnt_list = tng_data->molecule_cnt_list; - mols = &tng_data->molecules; - - return(TNG_SUCCESS); -} - -tng_function_status tng_util_trajectory_molecule_add(tng_trajectory_t tng_data, - const char *name, - const int64_t cnt, - tng_molecule_t *mol) -{ - tng_function_status stat; - stat = tng_molecule_add(tng_data, name, mol); - if(stat != TNG_SUCCESS) - { - return(stat); - } - stat = tng_molecule_cnt_set(tng_data, *mol, cnt); - - return(stat); -} - -tng_function_status tng_util_molecule_particles_get(tng_trajectory_t tng_data, - const tng_molecule_t mol, - int64_t *n_particles, - char ***names, - char ***types, - char ***res_names, - int64_t **res_ids, - char ***chain_names, - int64_t **chain_ids) -{ - tng_atom_t atom; - tng_residue_t res; - tng_chain_t chain; - int64_t i; - - *n_particles = mol->n_atoms; - - **names = malloc(sizeof(char *) * *n_particles); - **types = malloc(sizeof(char *) * *n_particles); - **res_names = malloc(sizeof(char *) * *n_particles); - **chain_names = malloc(sizeof(char *) * *n_particles); - *res_ids = malloc(sizeof(int64_t) * *n_particles); - *chain_ids = malloc(sizeof(int64_t) * *n_particles); - - for(i = 0; i < *n_particles; i++) - { - atom = &mol->atoms[i]; - res = atom->residue; - chain = res->chain; - *names[i] = malloc(strlen(atom->name)); - strcpy(*names[i], atom->name); - *types[i] = malloc(strlen(atom->atom_type)); - strcpy(*types[i], atom->atom_type); - *res_names[i] = malloc(strlen(res->name)); - strcpy(*res_names[i], res->name); - *chain_names[i] = malloc(strlen(chain->name)); - strcpy(*chain_names[i], chain->name); - *res_ids[i] = res->id; - *chain_ids[i] = chain->id; - } - - return(TNG_SUCCESS); -} - -tng_function_status tng_util_molecule_particles_set(tng_trajectory_t tng_data, - tng_molecule_t mol, - const int64_t n_particles, - const char **names, - const char **types, - const char **res_names, - const int64_t *res_ids, - const char **chain_names, - const int64_t *chain_ids) -{ - int64_t i; - tng_chain_t chain; - tng_residue_t residue; - tng_atom_t atom; - tng_function_status stat; - - for(i = 0; i < n_particles; i++) - { - if(tng_molecule_chain_find(tng_data, mol, chain_names[i], chain_ids[i], - &chain) == TNG_FAILURE) - { - stat = tng_molecule_chain_add(tng_data, mol, chain_names[i], - &chain); - if(stat != TNG_SUCCESS) - { - return(stat); - } - } - if(tng_chain_residue_find(tng_data, chain, res_names[i], res_ids[i], - &residue) == TNG_FAILURE) - { - stat = tng_chain_residue_add(tng_data, chain, res_names[i], - &residue); - if(stat != TNG_SUCCESS) - { - return(stat); - } - } - stat = tng_residue_atom_add(tng_data, residue, names[i], types[i], &atom); - if(stat != TNG_SUCCESS) - { - return(stat); - } - } - return(TNG_SUCCESS); -} - -tng_function_status tng_util_pos_read(tng_trajectory_t tng_data, - float *positions) -{ -} - -tng_function_status tng_util_vel_read(tng_trajectory_t tng_data, - float *velocities) -{ -} - -tng_function_status tng_util_force_read(tng_trajectory_t tng_data, - float *forces) -{ -} - -tng_function_status tng_util_pos_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *positions) -{ -} - -tng_function_status tng_util_vel_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *velocities) -{ -} - -tng_function_status tng_util_force_read_range(tng_trajectory_t tng_data, - const int64_t first_frame, - const int64_t last_frame, - float *forces) -{ -} - -tng_function_status tng_util_pos_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *positions) -{ -} - -tng_function_status tng_util_vel_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *velocities) -{ -} - -tng_function_status tng_util_force_write(tng_trajectory_t tng_data, - const int64_t frame_nr, - const float *forces) -{ -} - static TNG_INLINE int tng_min(int a, int b) { int r=a; @@ -3865,9 +3654,11 @@ static tng_function_status tng_particle_data_block_create static tng_function_status tng_compress(tng_trajectory_t tng_data, tng_gen_block_t block, - int64_t n_frames, - int64_t n_particles, - void *start_pos, int len) + const int64_t n_frames, + const int64_t n_particles, + const tng_data_type type, + void *start_pos, + const int len) { int nalgo; int new_len; @@ -3880,6 +3671,11 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, "TNG method.\n"); return(TNG_FAILURE); } + if(type != TNG_FLOAT_DATA && type != TNG_DOUBLE_DATA) + { + printf("Data type not supported.\n"); + return(TNG_FAILURE); + } if(block->id == TNG_TRAJ_POSITIONS) { @@ -3888,17 +3684,40 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, nalgo = tng_compress_nalgo(); tng_data->compress_algo_pos=malloc(nalgo * sizeof *tng_data->compress_algo_pos); - dest = tng_compress_pos_find_algo(start_pos, n_particles, - n_frames, - 0.01, 0, - tng_data->compress_algo_pos, - &new_len); + + if(type == TNG_FLOAT_DATA) + { + dest = tng_compress_pos_float_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data-> + compress_algo_pos, + &new_len); + } + else + { + dest = tng_compress_pos_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data-> + compress_algo_pos, + &new_len); + } } else { - dest = tng_compress_pos(start_pos, n_particles, - n_frames, 0.01, 0, - tng_data->compress_algo_pos, &new_len); + if(type == TNG_FLOAT_DATA) + { + dest = tng_compress_pos_float(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data->compress_algo_pos, &new_len); + } + else + { + dest = tng_compress_pos(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data->compress_algo_pos, &new_len); + } } } else @@ -3908,17 +3727,44 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, nalgo = tng_compress_nalgo(); tng_data->compress_algo_vel=malloc(nalgo * sizeof *tng_data->compress_algo_vel); - dest = tng_compress_vel_find_algo(start_pos, n_particles, - n_frames, - 0.01, 0, - tng_data->compress_algo_vel, - &new_len); + + if(type == TNG_FLOAT_DATA) + { + dest = tng_compress_vel_float_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data-> + compress_algo_vel, + &new_len); + } + else + { + dest = tng_compress_vel_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data-> + compress_algo_vel, + &new_len); + } } else { - dest = tng_compress_vel(start_pos, n_particles, - n_frames, 0.01, 0, - tng_data->compress_algo_vel, &new_len); + if(type == TNG_FLOAT_DATA) + { + dest = tng_compress_vel_float(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data-> + compress_algo_vel, + &new_len); + } + else + { + dest = tng_compress_vel(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data-> + compress_algo_vel, + &new_len); + } } } @@ -3944,12 +3790,14 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, static tng_function_status tng_uncompress(tng_trajectory_t tng_data, tng_gen_block_t block, + const tng_data_type type, void *start_pos, - unsigned long uncompressed_len) + const unsigned long uncompressed_len) { char *temp; - double *dest = 0; - int offset; + double *d_dest = 0; + float *f_dest = 0; + int offset, result; if(block->id != TNG_TRAJ_POSITIONS && block->id != TNG_TRAJ_VELOCITIES) @@ -3958,8 +3806,22 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, "TNG method.\n"); return(TNG_FAILURE); } + if(type != TNG_FLOAT_DATA && type != TNG_DOUBLE_DATA) + { + printf("Data type not supported.\n"); + return(TNG_FAILURE); + } - if(tng_compress_uncompress(start_pos, dest) == 1) + if(type == TNG_FLOAT_DATA) + { + result = tng_compress_uncompress_float(start_pos, f_dest); + } + else + { + result = tng_compress_uncompress(start_pos, d_dest); + } + + if(result == 1) { printf("Cannot uncompress TNG compressed block.\n"); return(TNG_FAILURE); @@ -3974,17 +3836,38 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, if(!temp) { free(block->block_contents); - free(dest); + if(d_dest) + { + free(d_dest); + } + if(f_dest) + { + free(f_dest); + } printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", block->block_contents_size, __FILE__, __LINE__); return(TNG_CRITICAL); } - memcpy(temp + offset, dest, uncompressed_len); + if(type == TNG_FLOAT_DATA) + { + memcpy(temp + offset, f_dest, uncompressed_len); + } + else + { + memcpy(temp + offset, d_dest, uncompressed_len); + } block->block_contents = temp; - free(dest); + if(d_dest) + { + free(d_dest); + } + if(f_dest) + { + free(f_dest); + } return(TNG_SUCCESS); } @@ -4207,6 +4090,122 @@ static tng_function_status tng_allocate_particle_data_mem return(TNG_SUCCESS); } +static tng_function_status tng_particle_data_find + (tng_trajectory_t tng_data, + const int64_t id, + tng_particle_data_t *data) +{ + int64_t block_index, i; + tng_trajectory_frame_set_t frame_set = &tng_data-> + current_trajectory_frame_set; + tng_block_type block_type_flag; + + if(tng_data->current_trajectory_frame_set_input_file_pos > 0 || + tng_data->current_trajectory_frame_set_output_file_pos > 0) + { + block_type_flag = TNG_TRAJECTORY_BLOCK; + } + else + { + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; + } + + block_index = -1; + if(block_type_flag == TNG_TRAJECTORY_BLOCK) + { + for(i = frame_set->n_particle_data_blocks; i-- ;) + { + *data = &frame_set->tr_particle_data[i]; + if((*data)->block_id == id) + { + block_index = i; + break; + } + } + } + else + { + for(i = tng_data->n_particle_data_blocks; i-- ;) + { + *data = &tng_data->non_tr_particle_data[i]; + if((*data)->block_id == id) + { + block_index = i; + break; + } + } + } + if(block_index == -1) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + +static tng_function_status tng_data_find + (tng_trajectory_t tng_data, + const int64_t id, + tng_non_particle_data_t *data) +{ + int64_t block_index, i; + tng_trajectory_frame_set_t frame_set = &tng_data-> + current_trajectory_frame_set; + tng_block_type block_type_flag; + + if(tng_data->current_trajectory_frame_set_input_file_pos > 0 || + tng_data->current_trajectory_frame_set_output_file_pos > 0) + { + block_type_flag = TNG_TRAJECTORY_BLOCK; + } + else + { + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; + } + + block_index = -1; + if(block_type_flag == TNG_TRAJECTORY_BLOCK) + { + for(i = frame_set->n_data_blocks; i-- ;) + { + *data = &frame_set->tr_data[i]; + if((*data)->block_id == id) + { + block_index = i; + break; + } + } + if(block_index == -1) + { + for(i = tng_data->n_data_blocks; i-- ;) + { + *data = &tng_data->non_tr_data[i]; + if((*data)->block_id == id) + { + block_index = i; + break; + } + } + } + } + else + { + for(i = tng_data->n_data_blocks; i-- ;) + { + *data = &tng_data->non_tr_data[i]; + if((*data)->block_id == id) + { + block_index = i; + break; + } + } + } + if(block_index == -1) + { + return(TNG_FAILURE); + } + return(TNG_SUCCESS); +} + /** Read the values of a particle data block * @param tng_data is a trajectory data container. * @param block is the block to store the data (should already contain @@ -4248,7 +4247,7 @@ static tng_function_status tng_particle_data_read const int64_t codec_id, const int64_t multiplier) { - int64_t block_index, i, j, k, tot_n_particles; + int64_t i, j, k, tot_n_particles; int size, len; unsigned long data_size; char ***first_dim_values, **second_dim_values; @@ -4273,45 +4272,18 @@ static tng_function_status tng_particle_data_read size = sizeof(double); } - if(tng_data->current_trajectory_frame_set_input_file_pos > 0) + /* If the block does not exist, create it */ + if(tng_particle_data_find(tng_data, block->id, &data) != TNG_SUCCESS) { - block_type_flag = TNG_TRAJECTORY_BLOCK; - } - else - { - block_type_flag = TNG_NON_TRAJECTORY_BLOCK; - } - - block_index = -1; - /* See if there is already a data block of this ID */ - if(block_type_flag == TNG_TRAJECTORY_BLOCK) - { - for(i = frame_set->n_particle_data_blocks; i-- ;) + if(tng_data->current_trajectory_frame_set_input_file_pos > 0) { - data = &frame_set->tr_particle_data[i]; - if(data->block_id == block->id) - { - block_index = i; - break; - } + block_type_flag = TNG_TRAJECTORY_BLOCK; } - } - else - { - for(i = tng_data->n_particle_data_blocks; i-- ;) + else { - data = &tng_data->non_tr_particle_data[i]; - if(data->block_id == block->id) - { - block_index = i; - break; - } + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; } - } - /* Otherwise create a data block */ - if(block_index == -1) - { if(tng_particle_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { @@ -4369,6 +4341,15 @@ static tng_function_status tng_particle_data_read printf("XTC compression not implemented yet.\n"); break; case TNG_TNG_COMPRESSION: + if(tng_uncompress(tng_data, block, datatype, + block->block_contents + *offset, + data_size) != TNG_SUCCESS) + { + printf("Could not read tng compressed block data. %s: %d\n", + __FILE__, __LINE__); + return(TNG_CRITICAL); + } + printf("TNG compression not implemented yet.\n"); break; #ifdef USE_ZLIB @@ -4911,29 +4892,41 @@ static tng_function_status tng_particle_data_block_write } - switch(data->codec_id) + if(frame_set->n_written_frames > 0) { - case TNG_XTC_COMPRESSION: - printf("XTC compression not implemented yet.\n"); - break; - case TNG_TNG_COMPRESSION: - printf("TNG compression not implemented yet.\n"); - break; -#ifdef USE_ZLIB - case TNG_GZIP_COMPRESSION: -// printf("Before compression: %"PRId64"\n", block->block_contents_size); - if(tng_gzip_compress(tng_data, block, - block->block_contents + data_start_pos, - block->block_contents_size - data_start_pos) != - TNG_SUCCESS) + switch(data->codec_id) { - printf("Could not write gzipped block data. %s: %d\n", __FILE__, - __LINE__); - return(TNG_CRITICAL); + case TNG_XTC_COMPRESSION: + printf("XTC compression not implemented yet.\n"); + break; + case TNG_TNG_COMPRESSION: + if(tng_compress(tng_data, block, data->n_frames / stride_length, + n_particles, data->datatype, + block->block_contents + data_start_pos, + block->block_contents_size - data_start_pos) != + TNG_SUCCESS) + { + printf("Could not write tng compressed block data. %s: %d\n", + __FILE__, __LINE__); + return(TNG_CRITICAL); + } + break; + #ifdef USE_ZLIB + case TNG_GZIP_COMPRESSION: + // printf("Before compression: %"PRId64"\n", block->block_contents_size); + if(tng_gzip_compress(tng_data, block, + block->block_contents + data_start_pos, + block->block_contents_size - data_start_pos) != + TNG_SUCCESS) + { + printf("Could not write gzipped block data. %s: %d\n", __FILE__, + __LINE__); + return(TNG_CRITICAL); + } + // printf("After compression: %"PRId64"\n", block->block_contents_size); + break; + #endif } -// printf("After compression: %"PRId64"\n", block->block_contents_size); - break; -#endif } if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS) @@ -5133,7 +5126,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, const int64_t codec_id, const int64_t multiplier) { - int64_t block_index, i, j; + int64_t i, j; int size, len; unsigned long data_size; tng_non_particle_data_t data; @@ -5143,15 +5136,6 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, // printf("%s\n", block->name); - if(tng_data->current_trajectory_frame_set_input_file_pos > 0) - { - block_type_flag = TNG_TRAJECTORY_BLOCK; - } - else - { - block_type_flag = TNG_NON_TRAJECTORY_BLOCK; - } - switch(datatype) { case TNG_CHAR_DATA: @@ -5168,37 +5152,18 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, size = sizeof(double); } - block_index = -1; - /* See if there is already a data block of this ID */ - /* FIXME: Do not compare with block->id. Use ID as parameter instead. */ - if(block_type_flag == TNG_TRAJECTORY_BLOCK) + /* If the block does not exist, create it */ + if(tng_data_find(tng_data, block->id, &data) != TNG_SUCCESS) { - for(i = frame_set->n_data_blocks; i-- ;) + if(tng_data->current_trajectory_frame_set_input_file_pos > 0) { - data = &frame_set->tr_data[i]; - if(data->block_id == block->id) - { - block_index = i; - break; - } + block_type_flag = TNG_TRAJECTORY_BLOCK; } - } - else - { - for(i = tng_data->n_data_blocks; i-- ;) + else { - data = &tng_data->non_tr_data[i]; - if(data->block_id == block->id) - { - block_index = i; - break; - } + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; } - } - /* Otherwise create a data block */ - if(block_index == -1) - { if(tng_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) { @@ -5240,7 +5205,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, data_size = (n_frames / stride_length) * size * n_values; switch(codec_id) { - #ifdef USE_ZLIB +#ifdef USE_ZLIB case TNG_GZIP_COMPRESSION: // printf("Before compression: %"PRId64"\n", block->block_contents_size); if(tng_gzip_uncompress(tng_data, block, @@ -5253,7 +5218,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, } // printf("After compression: %"PRId64"\n", block->block_contents_size); break; - #endif +#endif } } @@ -5707,23 +5672,26 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, memset(block->block_contents+offset, 0, block->block_contents_size - offset); } - switch(data->codec_id) + if(frame_set->n_written_frames > 0) { -#ifdef USE_ZLIB - case TNG_GZIP_COMPRESSION: -// printf("Before compression: %"PRId64"\n", block->block_contents_size); - if(tng_gzip_compress(tng_data, block, - block->block_contents + data_start_pos, - block->block_contents_size - data_start_pos) != - TNG_SUCCESS) + switch(data->codec_id) { - printf("Could not write gzipped block data. %s: %d\n", __FILE__, - __LINE__); - return(TNG_CRITICAL); + #ifdef USE_ZLIB + case TNG_GZIP_COMPRESSION: + // printf("Before compression: %"PRId64"\n", block->block_contents_size); + if(tng_gzip_compress(tng_data, block, + block->block_contents + data_start_pos, + block->block_contents_size - data_start_pos) != + TNG_SUCCESS) + { + printf("Could not write gzipped block data. %s: %d\n", __FILE__, + __LINE__); + return(TNG_CRITICAL); + } + // printf("After compression: %"PRId64"\n", block->block_contents_size); + break; + #endif } -// printf("After compression: %"PRId64"\n", block->block_contents_size); - break; -#endif } if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS) @@ -10285,11 +10253,10 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add const int64_t codec_id, void *new_data) { - int i, j, block_index, size, len; + int i, j, size, len; tng_trajectory_frame_set_t frame_set; tng_non_particle_data_t data; char **first_dim_values; - void *orig; char *new_data_c=new_data; frame_set = &tng_data->current_trajectory_frame_set; @@ -10299,36 +10266,8 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add stride_length = 1; } - block_index = -1; - /* See if there is already a data block of this ID */ - if(block_type_flag == TNG_TRAJECTORY_BLOCK) - { - for(i = frame_set->n_data_blocks; i-- ;) - { - data = &frame_set->tr_data[i]; - if(data->block_id == id) - { - block_index = i; - break; - } - } - } - else - { - n_frames = 1; - for(i = tng_data->n_data_blocks; i-- ;) - { - data = &tng_data->non_tr_data[i]; - if(data->block_id == id) - { - block_index = i; - break; - } - } - } - - /* Otherwise create a data block */ - if(block_index == -1) + /* If the block does not exist, create it */ + if(tng_data_find(tng_data, id, &data) != TNG_SUCCESS) { if(tng_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) @@ -10356,18 +10295,18 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add } strncpy(data->block_name, block_name, strlen(block_name) + 1); - data->datatype = datatype; - - data->stride_length = tng_max(stride_length, 1); data->values = 0; /* FIXME: Memory leak from strings. */ data->strings = 0; - data->n_values_per_frame = n_values_per_frame; - data->n_frames = n_frames; - data->codec_id = codec_id; - data->compression_multiplier = 1.0; } + data->datatype = datatype; + data->stride_length = tng_max(stride_length, 1); + data->n_values_per_frame = n_values_per_frame; + data->n_frames = n_frames; + data->codec_id = codec_id; + data->compression_multiplier = 1.0; + switch(datatype) { case TNG_FLOAT_DATA: @@ -10394,8 +10333,6 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add return(TNG_CRITICAL); } - orig = new_data_c; - if(n_frames > frame_set->n_written_frames) { frame_set->n_written_frames = n_frames; @@ -10451,12 +10388,11 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add const int64_t codec_id, void *new_data) { - int i, j, k, block_index, size, len; + int i, j, k, size, len; int64_t tot_n_particles; char ***first_dim_values, **second_dim_values; tng_trajectory_frame_set_t frame_set; tng_particle_data_t data; - char *orig; char *new_data_c=new_data; frame_set = &tng_data->current_trajectory_frame_set; @@ -10466,36 +10402,8 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add stride_length = 1; } - block_index = -1; - /* See if there is already a data block of this ID */ - if(block_type_flag == TNG_TRAJECTORY_BLOCK) - { - for(i = frame_set->n_particle_data_blocks; i-- ;) - { - data = &frame_set->tr_particle_data[i]; - if(data->block_id == id) - { - block_index = i; - break; - } - } - } - else - { - n_frames = 1; - for(i = tng_data->n_particle_data_blocks; i-- ;) - { - data = &tng_data->non_tr_particle_data[i]; - if(data->block_id == id) - { - block_index = i; - break; - } - } - } - - /* Otherwise create a data block */ - if(block_index == -1) + /* If the block does not exist, create it */ + if(tng_particle_data_find(tng_data, id, &data) != TNG_SUCCESS) { if(tng_particle_data_block_create(tng_data, block_type_flag) != TNG_SUCCESS) @@ -10527,15 +10435,16 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add data->datatype = datatype; - data->stride_length = tng_max(stride_length, 1); data->values = 0; /* FIXME: Memory leak from strings. */ data->strings = 0; - data->n_values_per_frame = n_values_per_frame; - data->n_frames = n_frames; - data->codec_id = codec_id; - data->compression_multiplier = 1.0; } + + data->stride_length = tng_max(stride_length, 1); + data->n_values_per_frame = n_values_per_frame; + data->n_frames = n_frames; + data->codec_id = codec_id; + data->compression_multiplier = 1.0; if(block_type_flag == TNG_TRAJECTORY_BLOCK && tng_data->var_num_atoms_flag) { @@ -10560,8 +10469,6 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add return(TNG_CRITICAL); } - orig = new_data_c; - if(n_frames > frame_set->n_written_frames) { frame_set->n_written_frames = n_frames; @@ -11777,26 +11684,39 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get tng_gen_block_t block; tng_function_status stat; - block_index = -1; - /* See if there is a data block of this ID. - * Start checking the last read frame set */ - for(i = frame_set->n_data_blocks; i-- ;) + if(tng_data_find(tng_data, block_id, &data) != TNG_SUCCESS) { - data = &frame_set->tr_data[i]; - if(data->block_id == block_id) + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set block */ + stat = tng_block_header_read(tng_data, block); + while(file_pos < tng_data->input_file_len && + stat != TNG_CRITICAL && + block->id != TNG_TRAJECTORY_FRAME_SET) { - block_index = i; - break; + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); } - } - if(block_index < 0) - { - /* If the data block was not found in the frame set - * look for it in the non-trajectory data (in tng_data). */ - for(i = tng_data->n_data_blocks; i-- ;) + for(i = frame_set->n_data_blocks; i-- ;) { - data = &tng_data->non_tr_data[i]; + data = &frame_set->tr_data[i]; if(data->block_id == block_id) { block_index = i; @@ -11805,47 +11725,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get } if(block_index < 0) { - tng_block_init(&block); - file_pos = ftell(tng_data->input_file); - /* Read all blocks until next frame set block */ - stat = tng_block_header_read(tng_data, block); - while(file_pos < tng_data->input_file_len && - stat != TNG_CRITICAL && - block->id != TNG_TRAJECTORY_FRAME_SET) - { - /* Use hash by default */ - stat = tng_block_read_next(tng_data, block, - TNG_USE_HASH); - if(stat != TNG_CRITICAL) - { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) - { - stat = tng_block_header_read(tng_data, block); - } - } - } - tng_block_destroy(&block); - if(stat == TNG_CRITICAL) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); - } - - for(i = frame_set->n_data_blocks; i-- ;) - { - data = &frame_set->tr_data[i]; - if(data->block_id == block_id) - { - block_index = i; - break; - } - } - if(block_index < 0) - { - return(TNG_FAILURE); - } + return(TNG_FAILURE); } } @@ -11919,37 +11799,52 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, const int64_t block_id, void **values, int64_t *n_frames, + int64_t *stride_length, int64_t *n_values_per_frame, tng_data_type *type) { - int64_t file_pos; - int i, block_index, data_size, size; + int64_t file_pos, data_size; + int i, block_index, size; tng_non_particle_data_t data; tng_trajectory_frame_set_t frame_set = &tng_data->current_trajectory_frame_set; tng_gen_block_t block; tng_function_status stat; + void *temp; - block_index = -1; - /* See if there is a data block of this ID. - * Start checking the last read frame set */ - for(i = frame_set->n_data_blocks; i-- ;) + if(tng_data_find(tng_data, block_id, &data) != TNG_SUCCESS) { - data = &frame_set->tr_data[i]; - if(data->block_id == block_id) + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set block */ + stat = tng_block_header_read(tng_data, block); + while(file_pos < tng_data->input_file_len && + stat != TNG_CRITICAL && + block->id != TNG_TRAJECTORY_FRAME_SET) { - block_index = i; - break; + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); } - } - if(block_index < 0) - { - /* If the data block was not found in the frame set - * look for it in the non-trajectory data (in tng_data). */ - for(i = tng_data->n_data_blocks; i-- ;) + for(i = frame_set->n_data_blocks; i-- ;) { - data = &tng_data->non_tr_data[i]; + data = &frame_set->tr_data[i]; if(data->block_id == block_id) { block_index = i; @@ -11958,47 +11853,7 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, } if(block_index < 0) { - tng_block_init(&block); - file_pos = ftell(tng_data->input_file); - /* Read all blocks until next frame set block */ - stat = tng_block_header_read(tng_data, block); - while(file_pos < tng_data->input_file_len && - stat != TNG_CRITICAL && - block->id != TNG_TRAJECTORY_FRAME_SET) - { - /* Use hash by default */ - stat = tng_block_read_next(tng_data, block, - TNG_USE_HASH); - if(stat != TNG_CRITICAL) - { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) - { - stat = tng_block_header_read(tng_data, block); - } - } - } - tng_block_destroy(&block); - if(stat == TNG_CRITICAL) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); - } - - for(i = frame_set->n_data_blocks; i-- ;) - { - data = &frame_set->tr_data[i]; - if(data->block_id == block_id) - { - block_index = i; - break; - } - } - if(block_index < 0) - { - return(TNG_FAILURE); - } + return(TNG_FAILURE); } } @@ -12021,11 +11876,21 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, *n_frames = tng_max(1, data->n_frames); *n_values_per_frame = data->n_values_per_frame; + *stride_length = data->stride_length; - data_size = (*n_frames / data->stride_length) * size * + data_size = (*n_frames / *stride_length) * size * *n_values_per_frame; - *values = malloc(data_size); + temp = realloc(*values, data_size); + if(!temp) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*values); + return(TNG_CRITICAL); + } + + *values = temp; memcpy(values, data->values, data_size); @@ -12218,6 +12083,121 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + union data_values ***values, + int64_t *n_values_per_frame, + tng_data_type *type) +{ + int64_t n_frames, tot_n_frames; + int64_t stride_length, current_frame_pos, data_size, frame_size; + int size; + tng_trajectory_frame_set_t frame_set; + tng_function_status stat; + void *current_values = 0, *temp; + + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + + frame_set = &tng_data->current_trajectory_frame_set; + + stat = tng_data_vector_get(tng_data, block_id, ¤t_values, + &n_frames, &stride_length, + n_values_per_frame, type); + + if(stat != TNG_SUCCESS) + { + if(current_values) + { + free(current_values); + } + return(stat); + } + + tot_n_frames = end_frame_nr - start_frame_nr + 1; + switch(*type) + { + case TNG_CHAR_DATA: + return(TNG_FAILURE); + case TNG_INT_DATA: + size = sizeof(int64_t); + break; + case TNG_FLOAT_DATA: + size = sizeof(float); + break; + case TNG_DOUBLE_DATA: + default: + size = sizeof(double); + } + + data_size = (tot_n_frames / stride_length) * size * + (*n_values_per_frame); + + temp = realloc(*values, data_size); + if(!temp) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*values); + return(TNG_CRITICAL); + } + + *values = temp; + + current_frame_pos = start_frame_nr - frame_set->first_frame; + + frame_size = size * (*n_values_per_frame); + + memcpy(*values, current_values + current_frame_pos * frame_size, + frame_size * (frame_set->n_frames - frame_set->first_frame - + current_frame_pos)); + + current_frame_pos += frame_set->n_frames - frame_set->first_frame - + current_frame_pos; + + while(current_frame_pos <= end_frame_nr) + { + stat = tng_frame_set_read_next(tng_data, hash_mode); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + stat = tng_data_vector_get(tng_data, block_id, ¤t_values, + &n_frames, &stride_length, + n_values_per_frame, type); + + if(stat != TNG_SUCCESS) + { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; + return(stat); + } + + memcpy(*values + (current_frame_pos - start_frame_nr) / stride_length, + current_values, + frame_size * (frame_set->n_frames - frame_set->first_frame - + current_frame_pos) / stride_length); + + current_frame_pos += frame_set->n_frames; + } + + free(current_values); + + return(TNG_SUCCESS); +} tng_function_status DECLSPECDLLEXPORT tng_particle_data_get (tng_trajectory_t tng_data, @@ -12238,79 +12218,58 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get tng_block_type block_type_flag; - block_index = -1; - - /* See if there is already a data block of this ID. - * Start checking the last read frame set */ - for(i = frame_set->n_particle_data_blocks; i-- ;) + if(tng_particle_data_find(tng_data, block_id, &data) != TNG_SUCCESS) { - data = &frame_set->tr_particle_data[i]; - if(data->block_id == block_id) + if(tng_data->current_trajectory_frame_set_input_file_pos > 0) { - block_index = i; block_type_flag = TNG_TRAJECTORY_BLOCK; - break; } - } + else + { + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; + } - if(block_index < 0) - { - /* If the data block was not found in the frame set - * look for it in the non-trajectory data (in tng_data). */ - for(i = tng_data->n_particle_data_blocks; i-- ;) + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set block */ + stat = tng_block_header_read(tng_data, block); + while(file_pos < tng_data->input_file_len && + stat != TNG_CRITICAL && + block->id != TNG_TRAJECTORY_FRAME_SET) + { + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) { - data = &tng_data->non_tr_particle_data[i]; + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } + + for(i = frame_set->n_particle_data_blocks; i-- ;) + { + data = &frame_set->tr_particle_data[i]; if(data->block_id == block_id) { block_index = i; - block_type_flag = TNG_NON_TRAJECTORY_BLOCK; + block_type_flag = TNG_TRAJECTORY_BLOCK; break; } } if(block_index < 0) { - tng_block_init(&block); - file_pos = ftell(tng_data->input_file); - /* Read all blocks until next frame set block */ - stat = tng_block_header_read(tng_data, block); - while(file_pos < tng_data->input_file_len && - stat != TNG_CRITICAL && - block->id != TNG_TRAJECTORY_FRAME_SET) - { - /* Use hash by default */ - stat = tng_block_read_next(tng_data, block, - TNG_USE_HASH); - if(stat != TNG_CRITICAL) - { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) - { - stat = tng_block_header_read(tng_data, block); - } - } - } - tng_block_destroy(&block); - if(stat == TNG_CRITICAL) - { - printf("Cannot read block header at pos %"PRId64". %s: %d\n", - file_pos, __FILE__, __LINE__); - return(stat); - } - - for(i = frame_set->n_particle_data_blocks; i-- ;) - { - data = &frame_set->tr_particle_data[i]; - if(data->block_id == block_id) - { - block_index = i; - block_type_flag = TNG_TRAJECTORY_BLOCK; - break; - } - } - if(block_index < 0) - { - return(TNG_FAILURE); - } + return(TNG_FAILURE); } } @@ -12419,6 +12378,150 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get + (tng_trajectory_t tng_data, + const int64_t block_id, + void **values, + int64_t *n_frames, + int64_t *stride_length, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type) +{ + int64_t i, j, mapping, file_pos, i_step, data_size; + int block_index, size; + tng_particle_data_t data; + tng_trajectory_frame_set_t frame_set = + &tng_data->current_trajectory_frame_set; + tng_gen_block_t block; + tng_function_status stat; + void *temp; + + tng_block_type block_type_flag; + + if(tng_particle_data_find(tng_data, block_id, &data) != TNG_SUCCESS) + { + if(tng_data->current_trajectory_frame_set_input_file_pos > 0) + { + block_type_flag = TNG_TRAJECTORY_BLOCK; + } + else + { + block_type_flag = TNG_NON_TRAJECTORY_BLOCK; + } + + tng_block_init(&block); + file_pos = ftell(tng_data->input_file); + /* Read all blocks until next frame set block */ + stat = tng_block_header_read(tng_data, block); + while(file_pos < tng_data->input_file_len && + stat != TNG_CRITICAL && + block->id != TNG_TRAJECTORY_FRAME_SET) + { + /* Use hash by default */ + stat = tng_block_read_next(tng_data, block, + TNG_USE_HASH); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + tng_block_destroy(&block); + if(stat == TNG_CRITICAL) + { + printf("Cannot read block header at pos %"PRId64". %s: %d\n", + file_pos, __FILE__, __LINE__); + return(stat); + } + + for(i = frame_set->n_particle_data_blocks; i-- ;) + { + data = &frame_set->tr_particle_data[i]; + if(data->block_id == block_id) + { + block_index = i; + block_type_flag = TNG_TRAJECTORY_BLOCK; + break; + } + } + if(block_index < 0) + { + return(TNG_FAILURE); + } + } + + if(block_type_flag == TNG_TRAJECTORY_BLOCK && + tng_data->var_num_atoms_flag) + { + *n_particles = frame_set->n_particles; + } + else + { + *n_particles = tng_data->n_particles; + } + + *type = data->datatype; + + switch(*type) + { + case TNG_CHAR_DATA: + return(TNG_FAILURE); + case TNG_INT_DATA: + size = sizeof(int64_t); + break; + case TNG_FLOAT_DATA: + size = sizeof(float); + break; + case TNG_DOUBLE_DATA: + default: + size = sizeof(double); + } + + *n_frames = tng_max(1, data->n_frames); + *n_values_per_frame = data->n_values_per_frame; + *stride_length = data->stride_length; + + data_size = (*n_frames / *stride_length) * size * (*n_particles) * + (*n_values_per_frame); + + temp = realloc(*values, data_size); + if(!temp) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*values); + return(TNG_CRITICAL); + } + + *values = temp; + + if(frame_set->n_mapping_blocks <= 0) + { + memcpy(values, data->values, data_size); + } + else + { + i_step = (*n_particles) * (*n_values_per_frame); + for(i = *n_frames; i--;) + { + for(j = *n_particles; j--;) + { + tng_particle_mapping_get_real_particle(frame_set, j, &mapping); + memcpy(values + size * (i * i_step + mapping * + (*n_values_per_frame)), + data->values + size * + (i * i_step + j * (*n_values_per_frame)), + size * (*n_values_per_frame)); + } + } + } + + return(TNG_SUCCESS); +} tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get (tng_trajectory_t tng_data, @@ -12645,6 +12748,122 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get + (tng_trajectory_t tng_data, + const int64_t block_id, + const int64_t start_frame_nr, + const int64_t end_frame_nr, + const tng_hash_mode hash_mode, + void **values, + int64_t *n_particles, + int64_t *n_values_per_frame, + tng_data_type *type) +{ + int64_t n_frames, tot_n_frames; + int64_t stride_length, current_frame_pos, data_size, frame_size; + int size; + tng_trajectory_frame_set_t frame_set; + tng_function_status stat; + void *current_values = 0, *temp; + + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + frame_set = &tng_data->current_trajectory_frame_set; + + stat = tng_particle_data_vector_get(tng_data, block_id, ¤t_values, + &n_frames, &stride_length, n_particles, + n_values_per_frame, type); + + if(stat != TNG_SUCCESS) + { + if(current_values) + { + free(current_values); + } + return(stat); + } + + tot_n_frames = end_frame_nr - start_frame_nr + 1; + switch(*type) + { + case TNG_CHAR_DATA: + return(TNG_FAILURE); + case TNG_INT_DATA: + size = sizeof(int64_t); + break; + case TNG_FLOAT_DATA: + size = sizeof(float); + break; + case TNG_DOUBLE_DATA: + default: + size = sizeof(double); + } + + data_size = (tot_n_frames / stride_length) * size * (*n_particles) * + (*n_values_per_frame); + + temp = realloc(*values, data_size); + if(!temp) + { + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + data_size, __FILE__, __LINE__); + free(*values); + return(TNG_CRITICAL); + } + + *values = temp; + + current_frame_pos = start_frame_nr - frame_set->first_frame; + + frame_size = size * (*n_particles) * (*n_values_per_frame); + + memcpy(*values, current_values + current_frame_pos * frame_size, + frame_size * (frame_set->n_frames - frame_set->first_frame - + current_frame_pos)); + + current_frame_pos += frame_set->n_frames - frame_set->first_frame - + current_frame_pos; + + while(current_frame_pos <= end_frame_nr) + { + stat = tng_frame_set_read_next(tng_data, hash_mode); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + stat = tng_particle_data_vector_get(tng_data, block_id, ¤t_values, + &n_frames, &stride_length, n_particles, + n_values_per_frame, type); + + if(stat != TNG_SUCCESS) + { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; + return(stat); + } + + memcpy(*values + (current_frame_pos - start_frame_nr) / stride_length, + current_values, + frame_size * (frame_set->n_frames - frame_set->first_frame - + current_frame_pos) / stride_length); + + current_frame_pos += frame_set->n_frames; + } + + free(current_values); + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_time_get_str (const tng_trajectory_t tng_data, @@ -12665,6 +12884,389 @@ tng_function_status DECLSPECDLLEXPORT tng_time_get_str } +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open + (const char *filename, + const char mode, + tng_trajectory_t *tng_data_p) +{ + if(mode != 'r' && mode != 'w' && mode != 'a') + { + return(TNG_FAILURE); + } + + if(tng_trajectory_init(tng_data_p) != TNG_SUCCESS) + { + tng_trajectory_destroy(tng_data_p); + return(TNG_CRITICAL); + } + + if(mode == 'r' || mode == 'a') + { + tng_input_file_set(*tng_data_p, filename); + + // Read the file headers + tng_file_headers_read(*tng_data_p, TNG_USE_HASH); + } + + if(mode == 'w' || mode == 'a') + { + tng_output_file_set(*tng_data_p, filename); + } + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close + (tng_trajectory_t *tng_data_p) +{ + return(tng_trajectory_destroy(tng_data_p)); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get + (tng_trajectory_t tng_data, + int64_t *n_mols, + int64_t *molecule_cnt_list, + tng_molecule_t *mols) +{ + /* FIXME: This should return a copy of the molecules instead */ + *n_mols = tng_data->n_molecules; + + molecule_cnt_list = tng_data->molecule_cnt_list; + mols = &tng_data->molecules; + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add + (tng_trajectory_t tng_data, + const char *name, + const int64_t cnt, + tng_molecule_t *mol) +{ + tng_function_status stat; + stat = tng_molecule_add(tng_data, name, mol); + if(stat != TNG_SUCCESS) + { + return(stat); + } + stat = tng_molecule_cnt_set(tng_data, *mol, cnt); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get + (tng_trajectory_t tng_data, + const tng_molecule_t mol, + int64_t *n_particles, + char ***names, + char ***types, + char ***res_names, + int64_t **res_ids, + char ***chain_names, + int64_t **chain_ids) +{ + tng_atom_t atom; + tng_residue_t res; + tng_chain_t chain; + int64_t i; + + *n_particles = mol->n_atoms; + + **names = malloc(sizeof(char *) * *n_particles); + **types = malloc(sizeof(char *) * *n_particles); + **res_names = malloc(sizeof(char *) * *n_particles); + **chain_names = malloc(sizeof(char *) * *n_particles); + *res_ids = malloc(sizeof(int64_t) * *n_particles); + *chain_ids = malloc(sizeof(int64_t) * *n_particles); + + for(i = 0; i < *n_particles; i++) + { + atom = &mol->atoms[i]; + res = atom->residue; + chain = res->chain; + *names[i] = malloc(strlen(atom->name)); + strcpy(*names[i], atom->name); + *types[i] = malloc(strlen(atom->atom_type)); + strcpy(*types[i], atom->atom_type); + *res_names[i] = malloc(strlen(res->name)); + strcpy(*res_names[i], res->name); + *chain_names[i] = malloc(strlen(chain->name)); + strcpy(*chain_names[i], chain->name); + *res_ids[i] = res->id; + *chain_ids[i] = chain->id; + } + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set + (tng_trajectory_t tng_data, + tng_molecule_t mol, + const int64_t n_particles, + const char **names, + const char **types, + const char **res_names, + const int64_t *res_ids, + const char **chain_names, + const int64_t *chain_ids) +{ + int64_t i; + tng_chain_t chain; + tng_residue_t residue; + tng_atom_t atom; + tng_function_status stat; + + for(i = 0; i < n_particles; i++) + { + if(tng_molecule_chain_find(tng_data, mol, chain_names[i], chain_ids[i], + &chain) == TNG_FAILURE) + { + stat = tng_molecule_chain_add(tng_data, mol, chain_names[i], + &chain); + if(stat != TNG_SUCCESS) + { + return(stat); + } + } + if(tng_chain_residue_find(tng_data, chain, res_names[i], res_ids[i], + &residue) == TNG_FAILURE) + { + stat = tng_chain_residue_add(tng_data, chain, res_names[i], + &residue); + if(stat != TNG_SUCCESS) + { + return(stat); + } + } + stat = tng_residue_atom_add(tng_data, residue, names[i], types[i], &atom); + if(stat != TNG_SUCCESS) + { + return(stat); + } + } + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read + (tng_trajectory_t tng_data, + float *positions) +{ + int64_t n_frames, n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_num_frames_get(tng_data, &n_frames); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_POSITIONS, + 0, n_frames - 1, TNG_USE_HASH, + (void **)(&positions), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read + (tng_trajectory_t tng_data, + float *velocities) +{ + int64_t n_frames, n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_num_frames_get(tng_data, &n_frames); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_VELOCITIES, + 0, n_frames - 1, TNG_USE_HASH, + (void **)(&velocities), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read + (tng_trajectory_t tng_data, + float *forces) +{ + int64_t n_frames, n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_num_frames_get(tng_data, &n_frames); + if(stat != TNG_SUCCESS) + { + return(stat); + } + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_FORCES, + 0, n_frames - 1, TNG_USE_HASH, + (void **)(&forces), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *positions) +{ + int64_t n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_POSITIONS, + first_frame, last_frame, + TNG_USE_HASH, + (void **)(&positions), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *velocities) +{ + int64_t n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_VELOCITIES, + first_frame, last_frame, + TNG_USE_HASH, + (void **)(&velocities), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range + (tng_trajectory_t tng_data, + const int64_t first_frame, + const int64_t last_frame, + float *forces) +{ + int64_t n_particles, n_values_per_frame; + tng_data_type type; + tng_function_status stat; + + stat = tng_particle_data_vector_interval_get(tng_data, TNG_TRAJ_FORCES, + first_frame, last_frame, + TNG_USE_HASH, + (void **)(&forces), + &n_particles, + &n_values_per_frame, + &type); + + return(stat); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *positions) +{ + tng_trajectory_frame_set_t frame_set = &tng_data-> + current_trajectory_frame_set; + tng_particle_data_t data; + int64_t n_particles, n_frames = 10000, stride_length = 100, frame_pos; + tng_function_status stat; + + if(!frame_set) + { + stat = tng_frame_set_new(tng_data, 0, n_frames); + if(stat != TNG_SUCCESS) + { + printf("Cannot create frame set. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + } + if(frame_set->first_frame + n_frames < frame_nr) + { + stat = tng_frame_set_write(tng_data, TNG_USE_HASH); + if(stat != TNG_SUCCESS) + { + printf("Cannot write frame set. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + stat = tng_frame_set_new(tng_data, frame_set->first_frame + + n_frames + 1, n_frames); + if(stat != TNG_SUCCESS) + { + printf("Cannot create frame set. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + } + + frame_pos = (frame_nr - frame_set->first_frame) / stride_length; + + tng_num_particles_get(tng_data, &n_particles); + + if(tng_particle_data_find(tng_data, TNG_TRAJ_POSITIONS, &data) + != TNG_SUCCESS) + { + stat = tng_particle_data_block_add(tng_data, TNG_TRAJ_POSITIONS, + "POSITIONS", + TNG_FLOAT_DATA, + TNG_TRAJECTORY_BLOCK, + n_frames, 3, stride_length, + 0, n_particles, + TNG_TNG_COMPRESSION, 0); + if(stat != TNG_SUCCESS) + { + printf("Error adding positions data block. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + stat = tng_allocate_particle_data_mem(tng_data, data, n_frames, + stride_length, n_particles, + 3); + } + memcpy(data->values + sizeof(float) * frame_pos, positions, + sizeof(float) * 3 * n_particles); + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *velocities) +{ +} + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *forces) +{ +} + + #ifdef BUILD_FORTRAN /* The following is for calling the library from fortran */ diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index 133a1fb..6e8efb6 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -459,15 +459,15 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) data[cnt++] = molpos[nr + 1] - 1; data[cnt++] = molpos[nr + 2] - 1; } -// if(tng_frame_particle_data_write(traj, frame_nr + i, -// TNG_TRAJ_POSITIONS, j * 300, 300, -// data, TNG_SKIP_HASH) != TNG_SUCCESS) -// { -// printf("Error adding data. %s: %d\n", __FILE__, __LINE__); -// free(molpos); -// free(data); -// return(TNG_CRITICAL); -// } + if(tng_frame_particle_data_write(traj, frame_nr + i, + TNG_TRAJ_POSITIONS, j * 300, 300, + data, TNG_SKIP_HASH) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + free(molpos); + free(data); + return(TNG_CRITICAL); + } } } |