diff options
| -rw-r--r-- | include/tng_io.h | 710 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 204 |
2 files changed, 834 insertions, 80 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 07ce96e..3145716 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -56,6 +56,7 @@ * * @section install_sec Installation * + * \code * mkdir build * * cd build @@ -64,9 +65,12 @@ * * make * + * make install + * \endcode * Test by running: - * + * \code * bin/tests/tng_testing + * \endcode * * @section change_sec Change Log * @@ -75,6 +79,7 @@ * Revisions * * v. 1.4 - Changed from LGPL to the Revised BSD License. + * * - More flexible support for digital signatures in header. * - Block ID numbers changed. * @@ -543,6 +548,7 @@ extern "C" /** * @brief Setup a trajectory data container. * @param tng_data_p a pointer to memory to initialise as a trajectory. + * @pre tng_data_p must not be pointing at a reserved memory block. * @details Memory is allocated during initialisation. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. @@ -568,6 +574,9 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy * end of the parallel block. * @param src the original trajectory. * @param dest_p a pointer to memory to initialise as a trajectory. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre tng_data_p must not be pointing at a reserved memory block. * @details Memory is allocated during initialisation. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. @@ -582,6 +591,10 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for file_name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code file_name != 0 \endcode The pointer to the file name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -593,6 +606,10 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_get * @brief Set the name of the input file. * @param tng_data the trajectory of which to set the input file name. * @param file_name the name of the input file. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code file_name != 0 \endcode The pointer to the file name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -607,6 +624,10 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for file_name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code file_name != 0 \endcode The pointer to the file name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -618,6 +639,10 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_get * @brief Set the name of the output file. * @param tng_data the trajectory of which to set the output file name. * @param file_name the name of the output file. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code file_name != 0 \endcode The pointer to the file name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -630,6 +655,10 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_set * @param tng_data the trajectory of which to get the endianness of the current * output file. * @param endianness will contain the enumeration of the endianness. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code endianness != 0 \endcode The pointer to the endianness container + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the endianness * could not be retrieved. */ @@ -642,6 +671,8 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_get * output file. * @param endianness the enumeration of the endianness, can be either * TNG_BIG_ENDIAN (0) or TNG_LITTLE_ENDIAN (1). + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @details The endianness cannot be changed after file output has started. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if the endianness * could not be set. @@ -657,6 +688,10 @@ tng_function_status DECLSPECDLLEXPORT tng_output_file_endianness_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -668,6 +703,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_get * @brief Set the name of the program used when creating the trajectory. * @param tng_data the trajectory of which to set the program name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -682,6 +721,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_program_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -693,6 +736,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_get * @brief Set the name of the program used when last modifying the trajectory. * @param tng_data the trajectory of which to set the program name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -707,6 +754,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_program_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -718,6 +769,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_get * @brief Set the name of the user who created the trajectory. * @param tng_data the trajectory of which to set the user name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -732,6 +787,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_user_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -743,6 +802,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_get * @brief Set the name of the user who last modified the trajectory. * @param tng_data the trajectory of which to set the user name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -757,6 +820,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_user_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -768,6 +835,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_get * @brief Set the name of the computer used when creating the trajectory. * @param tng_data the trajectory of which to set the computer name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -782,6 +853,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_computer_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -793,6 +868,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_get * @brief Set the name of the computer used when last modifying the trajectory. * @param tng_data the trajectory of which to set the computer name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -807,6 +886,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_computer_name_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code signature != 0 \endcode The pointer to the signature + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -818,6 +901,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_get * @brief Set the pgp_signature of the user creating the trajectory. * @param tng_data the trajectory of which to set the computer name. * @param signature is a string containing the pgp_signature. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code signature != 0 \endcode The pointer to the signature + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -832,6 +919,10 @@ tng_function_status DECLSPECDLLEXPORT tng_first_signature_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code signature != 0 \endcode The pointer to the signature + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -843,6 +934,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_get * @brief Set the pgp_signature of the user last modifying the trajectory. * @param tng_data the trajectory of which to set the computer name. * @param signature is a string containing the pgp_signature. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code signature != 0 \endcode The pointer to the signature + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -857,6 +952,10 @@ tng_function_status DECLSPECDLLEXPORT tng_last_signature_set * memory must be allocated before. * @param max_len maximum char length of the string, i.e. how much memory has * been reserved for name. This includes \0 terminating character. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (source string longer than destination string). */ @@ -868,6 +967,10 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_get * @brief Set the name of the forcefield used in the trajectory. * @param tng_data the trajectory of which to set the forcefield name. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the new_name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -879,6 +982,9 @@ tng_function_status DECLSPECDLLEXPORT tng_forcefield_name_set * @brief Get the medium stride length of the trajectory. * @param tng_data is the trajectory from which to get the stride length. * @param len is pointing to a value set to the stride length. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code len != 0 \endcode The pointer to len must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get @@ -889,6 +995,8 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_get * @brief Set the medium stride length of the trajectory. * @param tng_data is the trajectory of which to set the stride length. * @param len is the wanted medium stride length. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ @@ -900,6 +1008,9 @@ tng_function_status DECLSPECDLLEXPORT tng_medium_stride_length_set * @brief Get the long stride length of the trajectory. * @param tng_data is the trajectory from which to get the stride length. * @param len is pointing to a value set to the stride length. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code len != 0 \endcode The pointer to len must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get @@ -910,6 +1021,8 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_get * @brief Set the long stride length of the trajectory. * @param tng_data is the trajectory of which to set the stride length. * @param len is the wanted long stride length. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ @@ -921,6 +1034,9 @@ tng_function_status DECLSPECDLLEXPORT tng_long_stride_length_set * @brief Get the current time per frame of the trajectory. * @param tng_data is the trajectory from which to get the time per frame. * @param time is pointing to a value set to the time per frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code time != 0 \endcode The pointer to time must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get @@ -931,6 +1047,9 @@ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_get * @brief Set the time per frame of the trajectory. * @param tng_data is the trajectory of which to set the time per frame. * @param time is the new time per frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code time > 0 \endcode The time per frame must be >= 0. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred. */ @@ -942,6 +1061,9 @@ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set * @brief Get the length of the input file. * @param tng_data is the trajectory from which to get the input file length. * @param len is pointing to a value set to the file length. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code len != 0 \endcode The pointer to len must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get @@ -952,6 +1074,9 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get * @brief Get the number of frames in the trajectory * @param tng_data the trajectory of which to get the number of frames. * @param n is pointing to a value set to the number of frames. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred (could not find last frame set). */ @@ -963,6 +1088,8 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get * @brief Set the number of particles, in the case no molecular system is used. * @param tng_data is the trajectory of which to get the number of particles. * @param n is the number of particles to use. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @details When creating a molecular system the number of particles are set * automatically. This should only be used when there is no molecular system * specified or if the number of atoms needs to be overridden for some reason. @@ -976,6 +1103,9 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set * @brief Get the current number of particles. * @param tng_data is the trajectory from which to get the number of particles. * @param n is pointing to a value set to the number of particles. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @details If variable number of particles are used this function will return * the number of particles in the current frame set. * @return TNG_SUCCESS (0) if successful. @@ -988,6 +1118,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_particles_get * @brief Get the current total number of molecules. * @param tng_data is the trajectory from which to get the number of molecules. * @param n is pointing to a value set to the number of molecules. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @details If variable number of particles are used this function will return * the total number of molecules in the current frame set. * @return TNG_SUCCESS (0) if successful. @@ -1001,17 +1134,22 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get * @param mol_cnt_list is a list of the count of each molecule in the * mol system. This is a pointer to the list in the TNG container, which * means that it should be handled carefully. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE(1) if the list of * molecule counts was not valid. */ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_list_get (const tng_trajectory_t tng_data, - int64_t **mol_cnt_list); + int64_t *mol_cnt_list); /** * @brief Get the exponential used for distances in the trajectory. * @param tng_data is the trajectory from which to get the information. * @param exp is pointing to a value set to the distance unit exponential. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code exp != 0 \endcode The pointer to exp must not be a NULL pointer. * @details Example: If the distances are specified in nm (default) exp is -9. * If the distances are specified in Å exp is -10. * @return TNG_SUCCESS (0) if successful. @@ -1024,6 +1162,8 @@ tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_get * @brief Set the exponential used for distances in the trajectory. * @param tng_data is the trajectory of which to set the unit exponential. * @param exp is the distance unit exponential to use. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @details Example: If the distances are specified in nm (default) exp is -9. * If the distances are specified in Å exp is -10. * @return TNG_SUCCESS (0) if successful. @@ -1036,6 +1176,9 @@ tng_function_status DECLSPECDLLEXPORT tng_distance_unit_exponential_set * @brief Get the number of frames per frame set. * @param tng_data is the trajectory from which to get the number of frames * per frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @param n is pointing to a value set to the number of frames per frame set. * @return TNG_SUCCESS (0) if successful. */ @@ -1048,6 +1191,8 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_per_frame_set_get * @param tng_data is the trajectory of which to set the number of frames * per frame set. * @param n is the number of frames per frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @details This does not affect already existing frame sets. For * consistency the number of frames per frame set should be set * betfore creating any frame sets. @@ -1062,6 +1207,9 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_per_frame_set_set * @details This updates tng_data->n_trajectory_frame_sets before returning it. * @param tng_data is the trajectory from which to get the number of frame sets. * @param n is pointing to a value set to the number of frame sets. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n != 0 \endcode The pointer to n must not be a NULL pointer. * @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. */ @@ -1074,6 +1222,8 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get * @param tng_data is the trajectory from which to get the frame set. * @param frame_set_p will be set to point at the memory position of * the found frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get @@ -1084,6 +1234,9 @@ tng_function_status DECLSPECDLLEXPORT tng_current_frame_set_get * @brief Find the requested frame set number. * @param tng_data is the trajectory from which to get the frame set. * @param nr is the frame set number to search for. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code nr >= 0 \endcode The frame set number (nr) must be >= 0. * @details tng_data->current_trajectory_frame_set will contain the * found trajectory if successful. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -1097,6 +1250,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find * @brief Find the frame set containing a specific frame. * @param tng_data is the trajectory from which to get the frame set. * @param frame is the frame number to search for. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame >= 0 \endcode The frame number must be >= 0. * @details tng_data->current_trajectory_frame_set will contain the * found trajectory if successful. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -1112,6 +1268,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find * @param frame_set is the frame set of which to get the position of the * following frame set. * @param pos is pointing to a value set to the file position. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code pos != 0 \endcode The pointer to pos must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_next_frame_set_file_pos_get @@ -1125,6 +1284,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_next_frame_set_file_pos_get * @param frame_set is the frame set of which to get the position of the * previous frame set. * @param pos is pointing to a value set to the file position. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code pos != 0 \endcode The pointer to pos must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_prev_frame_set_file_pos_get @@ -1138,6 +1300,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_prev_frame_set_file_pos_get * @param frame_set is the frame set of which to get the frame range. * @param first_frame is set to the first frame of the frame set. * @param last_frame is set to the last frame of the frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code first_frame != 0 \endcode The pointer to first_frame must + * not be a NULL pointer. + * @pre \code last_frame != 0 \endcode The pointer to last_frame must + * not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_frame_range_get @@ -1175,6 +1343,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy * @param tng_data is the trajectory data container containing the block.. * @param name is a pointer to the string containing the name of the new molecule. * @param molecule is a pointer to the newly created molecule. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1189,6 +1361,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add * @param name is a pointer to the string containing the name of the new molecule. * @param id is the ID of the created molecule. * @param molecule is a pointer to the newly created molecule. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1203,6 +1379,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add * @param tng_data is the trajectory data container containing the molecule.. * @param molecule is the molecule to rename. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1216,6 +1396,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set * @param tng_data is the trajectory data container containing the molecule.. * @param molecule is the molecule of which to get the count. * @param cnt is a pointer to the variable to be populated with the count. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code cnt != 0 \endcode The pointer to the molecule count + * must not be a NULL pointer. * @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. */ @@ -1229,6 +1413,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get * @param tng_data is the trajectory data container containing the molecule.. * @param molecule is the molecule of which to set the count. * @param cnt is the number of instances of this molecule. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @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. */ @@ -1245,6 +1431,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_set * @param id is the id of the molecule to look for. If id is -1 only the name of * the molecule will be used for finding the molecule. * @param molecule is a pointer to the molecule if it was found - otherwise 0. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if the molecule is found or TNG_FAILURE (1) if the * molecule is not found. * @details If name is an empty string and id is -1 the first molecule will be @@ -1265,6 +1455,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_find * @param id is the id of the chain to look for. If id is -1 only the name of * the chain will be used for finding the chain. * @param chain is a pointer to the chain if it was found - otherwise 0. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if the chain is found or TNG_FAILURE (1) if the * chain is not found. * @details If name is an empty string and id is -1 the first chain will be @@ -1283,6 +1477,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find * @param molecule is the molecule to add a chain to. * @param name is a string containing the name of the chain. * @param chain is a pointer to the newly created chain. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1299,6 +1497,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add * @param name is a string containing the name of the chain. * @param id is the ID of the created chain. * @param chain is a pointer to the newly created chain. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1316,6 +1518,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add * @param from_atom_id is the id of one of the two atoms in the bond. * @param to_atom_id is the id of the other atom in the bond. * @param bond is a pointer to the newly created bond. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (!) if a minor error * has occured or TNG_CRITICAL (2) if a major error has occured. */ @@ -1331,6 +1535,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add * @param tng_data is the trajectory data container containing the atom.. * @param chain is the chain to rename. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1347,6 +1555,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set * @param id is the id of the residue to find. If id == -1 the first residue * that matches the specified name will be found. * @param residue is a pointer to the residue if it was found - otherwise 0. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if the residue is found or TNG_FAILURE (1) if the * residue is not found. * @details If name is an empty string the first residue will be found. @@ -1364,6 +1576,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find * @param chain is the chain to add a residue to. * @param name is a string containing the name of the residue. * @param residue is a pointer to the newly created residue. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1380,6 +1596,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add * @param name is a string containing the name of the residue. * @param id is the ID of the created residue. * @param residue is a pointer to the newly created residue. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1395,6 +1615,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add * @param tng_data is the trajectory data container containing the residue. * @param residue is the residue to rename. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The new name to set (new_name) must + * not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1410,6 +1634,12 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set * @param atom_name is a string containing the name of the atom. * @param atom_type is a string containing the atom type of the atom. * @param atom is a pointer to the newly created atom. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code atom_name != 0 \endcode The pointer to the atom name string + * must not be a NULL pointer. + * @pre \code atom_type != 0 \endcode The pointer to the atom_type string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1428,6 +1658,12 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add * @param atom_type is a string containing the atom type of the atom. * @param id is the ID of the created atom. * @param atom is a pointer to the newly created atom. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code atom_name != 0 \endcode The pointer to the atom name string + * must not be a NULL pointer. + * @pre \code atom_type != 0 \endcode The pointer to the atom_type string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if the ID could * not be set properly or TNG_CRITICAL (2) if a major error has occured. */ @@ -1444,6 +1680,10 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add * @param tng_data is the trajectory data container containing the atom. * @param atom is the atom to rename. * @param new_name is a string containing the wanted name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1457,6 +1697,10 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_set * @param tng_data is the trajectory data container containing the atom. * @param atom is the atom to change. * @param new_type is a string containing the atom type. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code new_type != 0 \endcode The pointer to the atom type string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1472,6 +1716,10 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_set * @param name is a string, which is set to the name of the molecule. Memory * must be reserved beforehand. * @param max_len is the maximum length of name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1486,6 +1734,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get * @param tng_data is the trajectory data container containing the atom. * @param nr is the real number of the particle in the molecular system. * @param id is will be set to the id of the molecule. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code id != 0 \endcode The pointer to id must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1504,6 +1755,14 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get * (number of atom in mol system) in bonds. * @param to_atoms is a list (memory reserved by this function) of atoms * (number of atom in mol system) in bonds. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_bonds != 0 \endcode The pointer to n_bonds must not be a + * NULL pointer. + * @pre \code from_atoms != 0 \endcode The pointer to from_atoms must not + * be a NULL pointer. + * @pre \code to_atoms != 0 \endcode The pointer to to_atoms must not + * be a NULL pointer. * @details The two lists of atoms use the same index, i.e. from_atoms[0] * and to_atoms[0] are linked with a bond. Since memory is reserved in * this function it must be freed afterwards. @@ -1523,6 +1782,10 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get * @param name is a string, which is set to the name of the chain. Memory * must be reserved beforehand. * @param max_len is the maximum length of name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1539,6 +1802,10 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get * @param name is a string, which is set to the name of the residue. Memory * must be reserved beforehand. * @param max_len is the maximum length of name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1554,6 +1821,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get * @param tng_data is the trajectory data container containing the atom. * @param nr is the real number of the particle in the molecular system. * @param id is a pointer to the variable, which will be set to the ID. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code id != 0 \endcode The pointer to id must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1568,6 +1838,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get * @param tng_data is the trajectory data container containing the atom. * @param nr is the real number of the particle in the molecular system. * @param id is a pointer to the variable, which will be set to the ID. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code id != 0 \endcode The pointer to id must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1583,6 +1856,10 @@ tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get * @param name is a string, which is set to the name of the atom. Memory * must be reserved beforehand. * @param max_len is the maximum length of name. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code name != 0 \endcode The pointer to the name string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1599,6 +1876,10 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get * @param type is a string, which is set to the type of the atom. Memory * must be reserved beforehand. * @param max_len is the maximum length of type. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code type != 0 \endcode The pointer to the type string + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (!) if a minor error * has occured. */ @@ -1617,11 +1898,13 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_of_particle_nr_get * the mapping block. * @details The mapping information is added to the currently active frame set * of tng_data - * @param first_particle_number is the first particle number of this mapping + * @param num_first_particle is the first particle number of this mapping * block. * @param n_particles is the number of particles in this mapping block. * @param mapping_table is a list of the real particle numbers (i.e. the numbers * used in the molecular system). The list is n_particles long. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @details mapping_table[0] is the real particle number of the first particle * in the following data blocks. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -1629,7 +1912,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_type_of_particle_nr_get */ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add (tng_trajectory_t tng_data, - const int64_t first_particle_number, + const int64_t num_first_particle, const int64_t n_particles, const int64_t *mapping_table); @@ -1644,6 +1927,8 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_mapping_add * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be * compared to the md5 hash of the read contents to ensure valid data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1661,6 +1946,8 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read * will be opened. * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @return TNG_SUCCESS (0) if successful or TNG_CRITICAL (2) if a major * error has occured. */ @@ -1681,6 +1968,10 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_write * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be * compared to the md5 hash of the read contents to ensure valid data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code block != 0 \endcode The block container (block) must be + * initialised before using it. * @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. */ @@ -1699,6 +1990,8 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be * compared to the md5 hash of the read contents to ensure valid data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @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. */ @@ -1715,6 +2008,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next * opened. * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH an md5 hash for each header block will be generated. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. * @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. */ @@ -1728,6 +2023,10 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_write * set. * @param first_frame is the first frame of the frame set. * @param n_frames is the number of frames in the frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code first_frame >= 0 \endcode The first frame must not be negative. + * @pre \code n_frames >= 0 \endcode The number of frames must not be negative. * @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. */ @@ -1744,6 +2043,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new * @param first_frame is the first frame of the frame set. * @param n_frames is the number of frames in the frame set. * @param first_frame_time is the time stamp of the first frame (in seconds). + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code first_frame >= 0 \endcode The first frame must not be negative. + * @pre \code n_frames >= 0 \endcode The number of frames must not be negative. + * @pre \code first_frame_time >= 0 \endcode The time stamp of the first frame + * must not be negative. * @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. */ @@ -1758,6 +2063,10 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new * @param tng_data is the trajectory containing the frame set. * @param first_frame_time is the time stamp of the first frame in the * frame set. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code first_frame_time >= 0 \endcode The time stamp of the first frame + * must not be negative. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set @@ -1782,6 +2091,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set * data block * @param codec_id is the ID of the codec to compress the data. * @param new_data is an array of data values to add. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code block_name != 0 \endcode The pointer to the block name must + * not be a NULL pointer. + * @pre \code n_values_per_frame > 0 \endcode n_values_per_frame must be + * a positive integer. * @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. */ @@ -1813,11 +2128,20 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add * for a box shape block) * @param stride_length is how many frames are between each entry in the * data block - * @param first_particle_number is the number of the first particle stored + * @param num_first_particle is the number of the first particle stored * in this data block * @param n_particles is the number of particles stored in this data block * @param codec_id is the ID of the codec to compress the data. * @param new_data is an array of data values to add. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code block_name != 0 \endcode The pointer to the block name must + * not be a NULL pointer. + * @pre \code n_values_per_frame > 0 \endcode n_values_per_frame must be + * a positive integer. + * @pre \code num_first_particle >= 0 \endcode The number of the + * first particle must be >= 0. + * @pre \code n_particles >= 0 \endcode n_particles must be >= 0. * @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. */ @@ -1830,7 +2154,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add int64_t n_frames, const int64_t n_values_per_frame, int64_t stride_length, - const int64_t first_particle_number, + const int64_t num_first_particle, const int64_t n_particles, const int64_t codec_id, void *new_data); @@ -1842,11 +2166,16 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add * will be opened. * @param frame_nr is the index number of the frame to write. * @param block_id is the ID of the data block to write the data to. - * @param data is an array of data to write. The length of the array should + * @param values is an array of data to write. The length of the array should * equal n_values_per_frame. * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be * compared to the md5 hash of the read contents to ensure valid data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values must not be a NULL + * pointer. * @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. */ @@ -1854,7 +2183,7 @@ 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 void *values, const char hash_mode); /** @@ -1868,11 +2197,19 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write * @param val_first_particle is the number of the first particle in the data * array. * @param val_n_particles is the number of particles in the data array. - * @param data is a 1D-array of data to write. The length of the array should + * @param values is a 1D-array of data to write. The length of the array should * equal n_particles * n_values_per_frame. * @param hash_mode is an option to decide whether to use the md5 hash or not. * If hash_mode == TNG_USE_HASH the written md5 hash in the file will be * compared to the md5 hash of the read contents to ensure valid data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code val_first_particle >= 0 \endcode The number of the + * first particle must be >= 0. + * @pre \code val_n_particles >= 0 \endcode The number of particles must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values must not be a NULL + * pointer. * @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. */ @@ -1882,7 +2219,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write const int64_t block_id, const int64_t val_first_particle, const int64_t val_n_particles, - const void *data, + const void *values, const char hash_mode); /** @@ -1935,6 +2272,14 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_frames != 0 \endcode The pointer to the number of frames + * must not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @details This function is obsolete and only retained for compatibility. Use * tng_data_vector_get() instead. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -1963,6 +2308,16 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get(tng_trajectory_t tng_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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_frames != 0 \endcode The pointer to the number of frames + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @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. @@ -1995,6 +2350,14 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @details This function is obsolete and only retained for compatibility. Use * tng_data_vector_interval_get() instead. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2031,6 +2394,16 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @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. @@ -2067,6 +2440,16 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_frames != 0 \endcode The pointer to the number of frames + * must not be a NULL pointer. + * @pre \code n_particles != 0 \endcode The pointer to the number of particles must + * not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @details This function is obsolete and only retained for compatibility. Use * tng_particle_data_vector_get() instead. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2103,6 +2486,16 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_particles != 0 \endcode The pointer to the number of particles must + * not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @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. @@ -2141,6 +2534,18 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_frames != 0 \endcode The pointer to the number of frames + * must not be a NULL pointer. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code n_particles != 0 \endcode The pointer to the number of particles must + * not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @details This function is obsolete and only retained for compatibility. Use * tng_particle_data_vector_interval_get() instead. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2184,6 +2589,18 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get * @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. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code n_particles != 0 \endcode The pointer to the number of particles must + * not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. + * @pre \code n_values_per_frame != 0 \endcode The pointer to the number of + * values per frame must not be a NULL pointer. + * @pre \code type != 0 \endcode The pointer to the data type must not + * be a NULL pointer. * @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. @@ -2200,10 +2617,15 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get int64_t *n_values_per_frame, char *type); -/** @brief Get the date and time of initial file creation in ISO format (string). - * @param tng_data is a trajectory data container. - * @param time is a pointer to the string in which the date will be stored. Memory - must be reserved beforehand. +/** + * @brief Get the date and time of initial file creation in ISO format (string). + * @param tng_data is a trajectory data container. + * @param time is a pointer to the string in which the date will be stored. Memory + * must be reserved beforehand. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code time != 0 \endcode The pointer to the time must not be a NULL + * pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_time_get_str @@ -2225,6 +2647,10 @@ tng_function_status DECLSPECDLLEXPORT tng_time_get_str * 'w' or 'a' for reading, writing or appending respectively. * @param tng_data_p is a pointer to the opened trajectory. This must be * closed by the user. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code filename != 0 \endcode The pointer to the filename must not be a + * NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2248,6 +2674,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close * @param tng_data is the trajectory containing the frame. * @param frame_nr is the frame number of which to get the time. * @param time is set to the time (in seconds) of the specified frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code time != 0 \endcode The pointer to the time must not be a + * NULL pointer. * @return TNG_SUCCESS (0) if successful or TNG_FAILURE (1) if a * minor error has occured. */ @@ -2263,6 +2693,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * @param molecule_cnt_list will be pointing to the list of counts of each molecule * in the mol system. * @param mols pointing to the list of molecules in the mol system. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code n_mols != 0 \endcode The pointer to the number of molecules must + * not be a NULL pointer. * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get @@ -2310,6 +2744,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get * The variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code positions != 0 \endcode The pointer to the positions array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2329,6 +2769,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read * variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code velocities != 0 \endcode The pointer to the velocities array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2348,6 +2794,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read * variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code forces != 0 \endcode The pointer to the forces array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2367,6 +2819,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read * If the box shape is not modified during the trajectory, but as general data, * that will be returned instead. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2388,6 +2846,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read * The variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code positions != 0 \endcode The pointer to the positions array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2411,6 +2877,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range * variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code velocities != 0 \endcode The pointer to the velocities array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2434,6 +2908,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range * variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code forces != 0 \endcode The pointer to the forces array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2459,6 +2941,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range * variable may point at already allocated memory or be a NULL pointer. * The memory must be freed afterwards. * @param stride_length will be set to the writing interval of the stored data. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code start_frame_nr <= end_frame_nr \endcode The first frame must be before + * the last frame. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array + * must not be a NULL pointer. + * @pre \code stride_length != 0 \endcode The pointer to the stride length + * must not be a NULL pointer. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error * has occured. @@ -2479,12 +2969,18 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -2511,12 +3007,18 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -2543,12 +3045,15 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -2573,6 +3078,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a positions data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2589,6 +3097,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a positions data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2605,6 +3116,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a positions data block if none exists. * This function is replaced by the more correcly named @@ -2623,6 +3137,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a velocities data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2639,6 +3156,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a velocities data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2673,6 +3193,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a forces data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2689,6 +3212,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a forces data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2723,6 +3249,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a box shape data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2739,6 +3268,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set * @param tng_data is the trajectory to use. * @param i is the output interval, i.e. i == 10 means data written every 10th * frame. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code i >= 0 \endcode The writing interval must be >= 0. * @details This function uses tng_util_generic_write_interval_set() and will * create a box shape data block if none exists. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2778,12 +3310,20 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_frequency_set * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values array must not + * be a NULL pointer. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -2816,12 +3356,20 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values array must not + * be a NULL pointer. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -2848,6 +3396,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write * @param frame_nr is the frame number of the data. * @param positions is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code positions != 0 \endcode The pointer to the positions array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a positions data block if none exists. Positions are stored as three * values per frame and compressed using TNG compression. @@ -2870,6 +3423,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write * @param frame_nr is the frame number of the data. * @param positions is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code positions != 0 \endcode The pointer to the positions array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a positions data block if none exists. Positions are stored as three * values per frame and compressed using TNG compression. @@ -2891,6 +3449,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write * @param frame_nr is the frame number of the data. * @param velocities is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code velocities != 0 \endcode The pointer to the velocities array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a velocities data block if none exists. Velocities are stored as three * values per frame and compressed using TNG compression. @@ -2913,6 +3476,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write * @param frame_nr is the frame number of the data. * @param velocities is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code velocities != 0 \endcode The pointer to the velocities array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a velocities data block if none exists. Velocities are stored as three * values per frame and compressed using TNG compression. @@ -2934,6 +3502,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write * @param frame_nr is the frame number of the data. * @param forces is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code forces != 0 \endcode The pointer to the forces array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a forces data block if none exists. Forces are stored as three * values per frame and compressed using gzip compression. @@ -2956,6 +3529,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write * @param frame_nr is the frame number of the data. * @param forces is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code forces != 0 \endcode The pointer to the forces array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a forces data block if none exists. Forces are stored as three * values per frame and compressed using gzip compression. @@ -2976,6 +3554,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. * @param box_shape is a 1D array of data to add. The array should be of length 9. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a box shape data block if none exists. Box shapes are stored as 9 * values per frame and compressed using TNG compression. @@ -2997,6 +3580,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write * @param tng_data is the trajectory to use. * @param frame_nr is the frame number of the data. * @param box_shape is a 1D array of data to add. The array should be of length 9. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not + * be a NULL pointer. * @details This function uses tng_util_generic_write() and will * create a box shape data block if none exists. Box shapes are stored as 9 * values per frame and compressed using TNG compression. @@ -3026,12 +3614,21 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values array must not + * be a NULL pointer. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -3067,12 +3664,21 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write * data is particle dependent there will be n_values_per_frame stored per * particle each frame. * @param block_id is the ID of the block, of which to set the output interval. - * @param block_name is a string that will be used as name of the block. + * @param block_name is a string that will be used as name of the block. Only + * required if the block did not exist, i.e. a new block is created. * @param particle_dependency should be TNG_NON_PARTICLE_BLOCK_DATA (0) if the * data is not related to specific particles (e.g. box shape) or * TNG_PARTICLE_BLOCK_DATA (1) is it is related to specific particles (e.g. - * positions). + * positions). Only required if the block did not exist, i.e. a new block is + * created. * @param compression is the compression routine to use when writing the data. + * Only required if the block did not exist, i.e. a new block is created. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code values != 0 \endcode The pointer to the values array must not + * be a NULL pointer. * @details n_values_per_frame, block_name, particle_dependency and * compression are only used if the data block did not exist before calling * this function, in which case it is created. @@ -3103,6 +3709,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write * @param time is the time stamp of the frame (in seconds). * @param positions is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code positions != 0 \endcode The pointer to the positions array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_write() and will * create a positions data block if none exists. Positions are stored as three * values per frame and compressed using TNG compression. @@ -3128,6 +3740,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write * @param time is the time stamp of the frame (in seconds). * @param positions is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code positions != 0 \endcode The pointer to the positions array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_double_write() and will * create a positions data block if none exists. Positions are stored as three * values per frame and compressed using TNG compression. @@ -3153,6 +3771,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write * @param time is the time stamp of the frame (in seconds). * @param velocities is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code velocities != 0 \endcode The pointer to the velocities array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_write() and will * create a velocities data block if none exists. Velocities are stored as three * values per frame and compressed using TNG compression. @@ -3178,6 +3802,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write * @param time is the time stamp of the frame (in seconds). * @param velocities is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code velocities != 0 \endcode The pointer to the velocities array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_double_write() and will * create a velocities data block if none exists. Velocities are stored as three * values per frame and compressed using TNG compression. @@ -3203,6 +3833,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write * @param time is the time stamp of the frame (in seconds). * @param forces is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code forces != 0 \endcode The pointer to the forces array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_write() and will * create a forces data block if none exists. Forces are stored as three * values per frame and compressed using gzip compression. @@ -3228,6 +3864,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write * @param time is the time stamp of the frame (in seconds). * @param forces is a 1D array of data to add. The array should be of length * n_particles * 3. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code forces != 0 \endcode The pointer to the forces array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_double_write() and will * create a forces data block if none exists. Forces are stored as three * values per frame and compressed using gzip compression. @@ -3252,6 +3894,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write * @param frame_nr is the frame number of the data. * @param time is the time stamp of the frame (in seconds). * @param box_shape is a 1D array of data to add. The array should be of length 9. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_write() and will * create a box shape data block if none exists. Box shapes are stored as 9 * values per frame and compressed using TNG compression. @@ -3276,6 +3924,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write * @param frame_nr is the frame number of the data. * @param time is the time stamp of the frame (in seconds). * @param box_shape is a 1D array of data to add. The array should be of length 9. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @pre \code frame_nr >= 0 \endcode The frame number to write must be >= 0. + * @pre \code time >= 0 \endcode The time stamp must be >= 0. + * @pre \code box_shape != 0 \endcode The pointer to the box_shape array must not + * be a NULL pointer. * @details This function uses tng_util_generic_with_time_double_write() and will * create a box shape data block if none exists. Box shapes are stored as 9 * values per frame and compressed using TNG compression. diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index efdee8c..5729297 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -6860,6 +6860,7 @@ tng_function_status tng_atom_name_set(tng_trajectory_t tng_data, (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(new_name, "TNG library: new_name must not be a NULL pointer."); len = tng_min_i((int)strlen(new_name) + 1, TNG_MAX_STR_LEN); @@ -6894,6 +6895,7 @@ tng_function_status tng_atom_type_set(tng_trajectory_t tng_data, (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(new_type, "TNG library: new_type must not be a NULL pointer."); len = tng_min_i((int)strlen(new_type) + 1, TNG_MAX_STR_LEN); @@ -6962,6 +6964,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_add tng_bool found_id = TNG_TRUE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); /* Find an unused ID */ id = 0; @@ -6996,6 +6999,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); new_molecules = realloc(tng_data->molecules, sizeof(struct tng_molecule) * @@ -7063,6 +7067,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(new_name, "TNG library: new_name must not be a NULL pointer."); len = tng_min_i((int)strlen(new_name) + 1, TNG_MAX_STR_LEN); @@ -7097,6 +7102,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_get int64_t i, index = -1; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(cnt, "TNG library: cnt must not be a NULL pointer."); for(i = tng_data->n_molecules; i--;) { @@ -7154,6 +7160,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_find int64_t i, n_molecules; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); n_molecules = tng_data->n_molecules; @@ -7185,6 +7192,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); n_chains = molecule->n_chains; @@ -7211,6 +7219,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_add const char *name, tng_chain_t *chain) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); + return(tng_molecule_chain_w_id_add(tng_data, molecule, name, molecule->n_chains + 1, chain)); } @@ -7227,6 +7238,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_w_id_add tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); new_chains = realloc(molecule->chains, sizeof(struct tng_chain) * @@ -7329,6 +7341,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(new_name, "TNG library: new_name must not be a NULL pointer."); len = tng_min_i((int)strlen(new_name) + 1, TNG_MAX_STR_LEN); @@ -7366,6 +7379,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); n_residues = chain->n_residues; @@ -7392,6 +7406,9 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_add const char *name, tng_residue_t *residue) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); + return(tng_chain_residue_w_id_add(tng_data, chain, name, chain->n_residues + 1, residue)); } @@ -7409,6 +7426,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add tng_function_status stat = TNG_SUCCESS; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); if(chain->n_residues) { @@ -7498,6 +7516,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_ (void)tng_data; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(new_name, "TNG library: new_name must not be a NULL pointer"); len = tng_min_i((int)strlen(new_name) + 1, TNG_MAX_STR_LEN); @@ -7531,6 +7550,10 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_add const char *atom_type, tng_atom_t *atom) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(atom_name, "TNG library: atom_name must not be a NULL pointer."); + TNG_ASSERT(atom_type, "TNG library: atom_type must not be a NULL pointer."); + return(tng_residue_atom_w_id_add(tng_data, residue, atom_name, atom_type, residue->chain->molecule->n_atoms + 1, atom)); @@ -7550,6 +7573,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add tng_function_status stat = TNG_SUCCESS; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(atom_name, "TNG library: atom_name must not be a NULL pointer."); + TNG_ASSERT(atom_type, "TNG library: atom_type must not be a NULL pointer."); if(!residue->n_atoms) { @@ -7690,8 +7715,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7729,8 +7755,9 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(id, "TNG library: id must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7765,8 +7792,11 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get tng_bond_t bond; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(n_bonds, "TNG library: n_bonds must not be a NULL pointer."); + TNG_ASSERT(from_atoms, "TNG library: from_atoms must not be a NULL pointer."); + TNG_ASSERT(to_atoms, "TNG library: to_atoms must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); *n_bonds = 0; /* First count the total number of bonds to allocate memory */ @@ -7827,8 +7857,9 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7873,8 +7904,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7918,8 +7950,9 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(id, "TNG library: id must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -7958,8 +7991,9 @@ tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(id, "TNG library: id must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -8002,8 +8036,9 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(name, "TNG library: name must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -8044,8 +8079,9 @@ tng_function_status tng_atom_type_of_particle_nr_get tng_bool found = TNG_FALSE; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(type, "TNG library: type must not be a NULL pointer."); - tng_molecule_cnt_list_get(tng_data, &molecule_cnt_list); + tng_molecule_cnt_list_get(tng_data, molecule_cnt_list); for(i = 0; i < tng_data->n_molecules; i++) { @@ -8697,7 +8733,6 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector tng_trajectory_t dest; TNG_ASSERT(src != 0, "TNG library: Source trajectory must not be NULL."); - TNG_ASSERT(*dest_p == 0, "TNG library: Pointer to tng_trajectory_t must be NULL to initialise the trajectory"); *dest_p = malloc(sizeof(struct tng_trajectory)); if(!*dest_p) @@ -9588,6 +9623,7 @@ tng_function_status DECLSPECDLLEXPORT tng_time_per_frame_set tng_trajectory_frame_set_t frame_set; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(time >= 0, "TNG library: The time per frame must be >= 0."); frame_set = &tng_data->current_trajectory_frame_set; @@ -9701,7 +9737,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(n, "TNG library: n must not be a NULL pointer"); - tng_molecule_cnt_list_get(tng_data, &cnt_list); + tng_molecule_cnt_list_get(tng_data, cnt_list); for(i = tng_data->n_molecules; i --;) { @@ -9715,18 +9751,20 @@ tng_function_status DECLSPECDLLEXPORT tng_num_molecules_get tng_function_status DECLSPECDLLEXPORT tng_molecule_cnt_list_get (const tng_trajectory_t tng_data, - int64_t **mol_cnt_list) + int64_t *mol_cnt_list) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + if(tng_data->var_num_atoms_flag) { - *mol_cnt_list = tng_data->current_trajectory_frame_set. - molecule_cnt_list; + mol_cnt_list = tng_data->current_trajectory_frame_set. + molecule_cnt_list; } else { - *mol_cnt_list = tng_data->molecule_cnt_list; + mol_cnt_list = tng_data->molecule_cnt_list; } - if(*mol_cnt_list == 0) + if(mol_cnt_list == 0) { return(TNG_FAILURE); } @@ -9943,6 +9981,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(nr >= 0, "The frame set number (nr) must be >= 0"); frame_set = &tng_data->current_trajectory_frame_set; @@ -10267,6 +10306,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_of_frame_find tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(frame >= 0, "TNG library: frame must be >= 0."); frame_set = &tng_data->current_trajectory_frame_set; @@ -10770,8 +10810,9 @@ tng_function_status DECLSPECDLLEXPORT tng_file_headers_read return(TNG_SUCCESS); } -tng_function_status DECLSPECDLLEXPORT tng_file_headers_write(tng_trajectory_t tng_data, - const char hash_mode) +tng_function_status DECLSPECDLLEXPORT tng_file_headers_write + (tng_trajectory_t tng_data, + const char hash_mode) { int i; tng_gen_block_t data_block; @@ -10861,8 +10902,6 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next(tng_trajectory_t t tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(tng_data->first_trajectory_frame_set_input_file_pos || tng_data->current_trajectory_frame_set.next_frame_set_file_pos, "TNG library: pos must not be a NULL pointer"); - if(tng_input_file_init(tng_data) != TNG_SUCCESS) { @@ -11049,8 +11088,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new int64_t curr_pos; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(first_frame >= 0, "TNG library: first_frame must be positive."); - TNG_ASSERT(n_frames >= 0, "TNG library: n_frames must be positive."); + TNG_ASSERT(first_frame >= 0, "TNG library: first_frame must be >= 0."); + TNG_ASSERT(n_frames >= 0, "TNG library: n_frames must be >= 0."); frame_set = &tng_data->current_trajectory_frame_set; @@ -11249,9 +11288,9 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_with_time_new tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(first_frame >= 0, "TNG library: first_frame must be positive."); - TNG_ASSERT(n_frames >= 0, "TNG library: n_frames must be positive."); - TNG_ASSERT(first_frame_time >= 0, "TNG library: first_frame_time must be positive."); + TNG_ASSERT(first_frame >= 0, "TNG library: first_frame must be >= 0."); + TNG_ASSERT(n_frames >= 0, "TNG library: n_frames must be >= 0."); + TNG_ASSERT(first_frame_time >= 0, "TNG library: first_frame_time must be >= 0."); stat = tng_frame_set_new(tng_data, first_frame, n_frames); @@ -11269,7 +11308,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_first_frame_time_set const double first_frame_time) { TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(first_frame_time >= 0, "TNG library: first_frame_time must be positive."); + TNG_ASSERT(first_frame_time >= 0, "TNG library: first_frame_time must be >= 0."); tng_data->current_trajectory_frame_set.first_frame_time = first_frame_time; @@ -11296,8 +11335,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add int64_t n_frames_div; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(block_name, "TNG library: block_name mustnot be a NULL pointer."); - TNG_ASSERT(n_frames > 0, "TNG library: n_frames must be a positive integer."); + TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer."); TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer."); frame_set = &tng_data->current_trajectory_frame_set; @@ -11443,7 +11481,6 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(block_name, "TNG library: block_name mustnot be a NULL pointer."); - TNG_ASSERT(n_frames > 0, "TNG library: n_frames must be a positive integer."); TNG_ASSERT(n_values_per_frame > 0, "TNG library: n_values_per_frame must be a positive integer."); TNG_ASSERT(num_first_particle >= 0, "TNG library: num_first_particle must be >= 0."); TNG_ASSERT(n_particles >= 0, "TNG library: n_particles must be >= 0."); @@ -14243,6 +14280,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open const char mode, tng_trajectory_t *tng_data_p) { + TNG_ASSERT(filename, "TNG library: filename must not be a NULL pointer."); + if(mode != 'r' && mode != 'w' && mode != 'a') { return(TNG_FAILURE); @@ -14305,6 +14344,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get { int64_t first_frame; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(time, "TNG library: time must not be a NULL pointer"); tng_trajectory_frame_set_t frame_set; @@ -14340,6 +14380,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get tng_trajectory_frame_set_t frame_set; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(n_mols, "TNG library: n_mols must not be a NULL pointer."); *n_mols = tng_data->n_molecules; @@ -14489,6 +14530,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); stat = tng_num_frames_get(tng_data, &n_frames); @@ -14516,6 +14559,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); stat = tng_num_frames_get(tng_data, &n_frames); @@ -14543,6 +14588,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); stat = tng_num_frames_get(tng_data, &n_frames); @@ -14571,6 +14618,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); stat = tng_num_frames_get(tng_data, &n_frames); @@ -14600,6 +14649,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); TNG_ASSERT(first_frame <= last_frame, "TNG library: first_frame must be lower or equal to last_frame."); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); @@ -14626,6 +14677,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); TNG_ASSERT(first_frame <= last_frame, "TNG library: first_frame must be lower or equal to last_frame."); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); @@ -14652,6 +14705,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); TNG_ASSERT(first_frame <= last_frame, "TNG library: first_frame must be lower or equal to last_frame."); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); @@ -14678,6 +14733,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range char type; tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); TNG_ASSERT(first_frame <= last_frame, "TNG library: first_frame must be lower or equal to last_frame."); TNG_ASSERT(stride_length, "TNG library: stride_length must not be a NULL pointer"); @@ -14708,8 +14765,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); + TNG_ASSERT(i >= 0, "TNG library: i (writing interval) must be >= 0."); if(i <= 0) { @@ -14743,12 +14799,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set != TNG_SUCCESS) { stat = tng_particle_data_block_add(tng_data, block_id, - block_name, - TNG_FLOAT_DATA, - TNG_TRAJECTORY_BLOCK, - n_frames, n_values_per_frame, i, - 0, n_particles, - compression, 0); + block_name, + TNG_FLOAT_DATA, + TNG_TRAJECTORY_BLOCK, + n_frames, n_values_per_frame, i, + 0, n_particles, + compression, 0); if(stat != TNG_SUCCESS) { printf("TNG library: Error %s adding data block. %s: %d\n", block_name, @@ -14769,7 +14825,19 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set } else { - p_data->stride_length = i; + if(p_data->stride_length != i) + { + p_data->stride_length = i; + stat = tng_allocate_particle_data_mem(tng_data, p_data, n_frames, + i, n_particles, + n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + } } } else @@ -14799,7 +14867,18 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_set } else { - np_data->stride_length = i; + if(np_data->stride_length != i) + { + np_data->stride_length = i; + stat = tng_allocate_data_mem(tng_data, np_data, n_frames, + i, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } + } } } @@ -14822,8 +14901,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_interval_double_set tng_function_status stat; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); - TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); + TNG_ASSERT(i >= 0, "TNG library: i (writing interval) must be >= 0."); if(i <= 0) { @@ -14940,6 +15018,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_set(tng_data, i, 3, @@ -14953,6 +15032,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_interval_double_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_double_set(tng_data, i, 3, @@ -14975,6 +15055,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_set(tng_data, i, 3, @@ -14988,6 +15069,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_interval_double_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_double_set(tng_data, i, 3, @@ -15010,6 +15092,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_set(tng_data, i, 3, @@ -15023,6 +15106,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write_interval_double_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_double_set(tng_data, i, 3, @@ -15045,6 +15129,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_set (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_set(tng_data, i, 9, @@ -15058,6 +15143,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write_interval_double_s (tng_trajectory_t tng_data, const int64_t i) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(i > 0, "TNG library: i (writing interval) must be >= 0."); return(tng_util_generic_write_interval_double_set(tng_data, i, 9, @@ -15096,7 +15182,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(values, "TNG library: values must not be a NULL pointer"); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); if(particle_dependency == TNG_PARTICLE_BLOCK_DATA) { @@ -15162,13 +15247,13 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write != TNG_SUCCESS) { stat = tng_particle_data_block_add(tng_data, block_id, - block_name, - TNG_FLOAT_DATA, - block_type_flag, - n_frames, n_values_per_frame, - stride_length, - 0, n_particles, - compression, 0); + block_name, + TNG_FLOAT_DATA, + block_type_flag, + n_frames, n_values_per_frame, + stride_length, + 0, n_particles, + compression, 0); if(stat != TNG_SUCCESS) { printf("TNG library: Error %s adding data block. %s: %d\n", block_name, @@ -15285,7 +15370,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(values, "TNG library: values must not be a NULL pointer"); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); if(particle_dependency == TNG_PARTICLE_BLOCK_DATA) { @@ -15459,6 +15543,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write const int64_t frame_nr, const float *positions) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); @@ -15473,6 +15558,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_double_write const int64_t frame_nr, const double *positions) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); @@ -15487,6 +15573,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_write const int64_t frame_nr, const float *velocities) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); @@ -15501,6 +15588,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_double_write const int64_t frame_nr, const double *velocities) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); @@ -15515,6 +15603,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write const int64_t frame_nr, const float *forces) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); @@ -15529,6 +15618,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_double_write const int64_t frame_nr, const double *forces) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); @@ -15543,6 +15633,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_write const int64_t frame_nr, const float *box_shape) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); @@ -15557,6 +15648,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_double_write const int64_t frame_nr, const double *box_shape) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); @@ -15579,10 +15671,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_write { tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(values, "TNG library: values must not be a NULL pointer"); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); stat = tng_util_generic_write(tng_data, frame_nr, values, n_values_per_frame, block_id, block_name, @@ -15613,10 +15705,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_with_time_double_write { tng_function_status stat; + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(values, "TNG library: values must not be a NULL pointer"); - TNG_ASSERT(block_name, "TNG library: block_name must not be a NULL pointer"); stat = tng_util_generic_double_write(tng_data, frame_nr, values, n_values_per_frame, block_id, block_name, @@ -15640,6 +15732,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_write const double time, const float *positions) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); @@ -15656,6 +15749,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_with_time_double_write const double time, const double *positions) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); @@ -15674,6 +15768,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_write const double time, const float *velocities) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); @@ -15692,6 +15787,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_with_time_double_write const double time, const double *velocities) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(velocities, "TNG library: velocities must not be a NULL pointer"); @@ -15710,6 +15806,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_write const double time, const float *forces) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); @@ -15726,6 +15823,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_with_time_double_write const double time, const double *forces) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(forces, "TNG library: forces must not be a NULL pointer"); @@ -15743,6 +15841,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_write const double time, const float *box_shape) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); @@ -15759,6 +15858,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write const double time, const double *box_shape) { + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(time >= 0, "TNG library: time must be >= 0."); TNG_ASSERT(box_shape, "TNG library: box_shape must not be a NULL pointer"); |