diff options
Diffstat (limited to 'include')
| -rw-r--r-- | include/tng_io.h | 45 |
1 files changed, 24 insertions, 21 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 832379b..07ce96e 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -344,9 +344,9 @@ typedef unsigned __int64 uint64_t; #define TNG_MAX_STR_LEN 1024 #ifndef NDEBUG -#define TNG_ASSERT(cnd, msg) if(!cnd) {printf("%s\n", msg); assert(cnd);} +#define TNG_ASSERT(cnd, msg) if(!(cnd)) {printf("%s\n", msg); assert(cnd);} #else -#define TNG_ASSERT(cnd, msg) ((void) 0) +#define TNG_ASSERT(cnd, msg) (void)0; #endif /** Flag to specify the endianness of a TNG file */ @@ -966,7 +966,7 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get * @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. - * @return TNG_SUCCESS (0) if succesful. + * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set (tng_trajectory_t tng_data, @@ -1001,7 +1001,7 @@ 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. - * @return TNG_SUCCESS (0) if succesful or TNG_FAILURE(1) if the list of + * @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 @@ -2260,22 +2260,16 @@ tng_function_status DECLSPECDLLEXPORT tng_util_time_of_frame_get * @brief High-level function for getting the molecules in the mol system. * @param tng_data is the trajectory containing the mol system. * @param n_mols is set to the number of molecules in the system. - * @param molecule_cnt_list will be a copy of the counts of each molecule + * @param molecule_cnt_list will be pointing to the list of counts of each molecule * in the mol system. - * @param mols will be a list of copies of the molecules in the mol system. - * @details Memory is reserved for molecule_cnt_list and mols in this function. - * If the pointers do not point at already allocated memory they must be NULL - * pointers so that new memory can be reserved. The memory of molecule_cnt_list - * and mols must be freed afterwards. - * mols will contain copies of the molecules in the mol system, but these - * molecules still contain pointers to the actual atoms and residues etc., which - * means that the data of the molecules should be handled with care. + * @param mols pointing to the list of molecules in the mol system. + * @return TNG_SUCCESS (0) if successful. */ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, - int64_t **molecule_cnt_list, - tng_molecule_t **mols); + int64_t *molecule_cnt_list, + tng_molecule_t *mols); /* // tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add @@ -2313,6 +2307,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get * @param positions will be set to point at a 1-dimensional array of floats, * which will contain the positions. The data is stored sequentially in order * of frames. For each frame the positions (x, y and z coordinates) are stored. + * 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2330,7 +2325,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read * @param tng_data is the trajectory to read from. * @param velocities will be set to point at a 1-dimensional array of floats, * which will contain the velocities. The data is stored sequentially in order - * of frames. For each frame the velocities (in x, y and z) are stored. + * of frames. For each frame the velocities (in x, y and z) are stored. 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2348,7 +2344,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read * @param tng_data is the trajectory to read from. * @param forces will be set to point at a 1-dimensional array of floats, * which will contain the forces. The data is stored sequentially in order - * of frames. For each frame the forces (in x, y and z) are stored. + * of frames. For each frame the forces (in x, y and z) are stored. 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2365,7 +2362,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read * @param tng_data is the trajectory to read from. * @param box_shape will be set to point at a 1-dimensional array of floats, * which will contain the box shape. The data is stored sequentially in order - * of frames. For each frame the box shape is stored as nine values. + * of frames. For each frame the box shape is stored as nine values. The + * variable may point at already allocated memory or be a NULL pointer. * 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. @@ -2387,6 +2385,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read * @param positions will be set to point at a 1-dimensional array of floats, * which will contain the positions. The data is stored sequentially in order * of frames. For each frame the positions (x, y and z coordinates) are stored. + * 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2408,7 +2407,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_read_range * @param last_frame is the last frame to return position data from. * @param velocities will be set to point at a 1-dimensional array of floats, * which will contain the velocities. The data is stored sequentially in order - * of frames. For each frame the velocities (in x, y and z) are stored. + * of frames. For each frame the velocities (in x, y and z) are stored. 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2430,7 +2430,8 @@ tng_function_status DECLSPECDLLEXPORT tng_util_vel_read_range * @param last_frame is the last frame to return position data from. * @param forces will be set to point at a 1-dimensional array of floats, * which will contain the forces. The data is stored sequentially in order - * of frames. For each frame the forces (in x, y and z) are stored. + * of frames. For each frame the forces (in x, y and z) are stored. 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. * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error @@ -2454,7 +2455,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range * which will contain the box shape. The data is stored sequentially in order * of frames. For each frame the box shape is stored as nine values. * If the box shape is not modified during the trajectory, but as general data, - * that will be returned instead. + * that will be returned instead. 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. * @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 |