diff options
| -rw-r--r-- | include/tng_io.h | 26 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 100 |
2 files changed, 101 insertions, 25 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 107e2d0..c6c961d 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1141,7 +1141,7 @@ 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); /** * @brief Get the exponential used for distances in the trajectory. @@ -2705,13 +2705,25 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get int64_t **molecule_cnt_list, tng_molecule_t **mols); + +/** + * @brief High-level function for adding a molecule to the mol system. + * @param tng_data is the trajectory containing the mol system. + * @param name is the name of the molecule to add. + * @param cnt is the count of the molecule. + * @param mol is set to point to the newly created molecule. + * @pre \code name != 0 \endcode The pointer to the name must not be a + * NULL pointer. + * @pre \code cnt >= 0 \endcode The requested count must be >= 0. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occured or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add + (tng_trajectory_t tng_data, + const char *name, + const int64_t cnt, + tng_molecule_t *mol); /* -// tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add -// (tng_trajectory_t tng_data, -// const char *name, -// const int64_t cnt, -// tng_molecule_t *mol); -// // tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get // (tng_trajectory_t tng_data, // const tng_molecule_t mol, diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 01ef8f0..d7c8b8b 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -7283,8 +7283,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_bond_add { int64_t i; tng_bond_t new_bonds; - - TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + (void)tng_data; for(i = 0; i < molecule->n_bonds; i++) { @@ -7709,7 +7708,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_of_particle_nr_get 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++) { @@ -7749,7 +7748,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_id_of_particle_nr_get 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++) { @@ -7788,7 +7787,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molsystem_bonds_get 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 */ @@ -7851,7 +7850,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_of_particle_nr_get 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++) { @@ -7898,7 +7897,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_of_particle_nr_get 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++) { @@ -7944,7 +7943,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_id_of_particle_nr_get 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++) { @@ -7985,7 +7984,7 @@ tng_function_status DECLSPECDLLEXPORT tng_global_residue_id_of_particle_nr_get 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++) { @@ -8030,7 +8029,7 @@ tng_function_status DECLSPECDLLEXPORT tng_atom_name_of_particle_nr_get 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++) { @@ -8073,7 +8072,7 @@ tng_function_status tng_atom_type_of_particle_nr_get 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++) { @@ -9696,7 +9695,72 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set (tng_trajectory_t tng_data, const int64_t n) { - tng_data->n_particles = n; + tng_molecule_t mol; + tng_chain_t chain; + tng_residue_t res; + tng_atom_t atom; + tng_function_status stat; + int64_t diff, n_mod; + + TNG_ASSERT(n >= 0, "TNG library: The number of molecules must be >= 0"); + + diff = n - tng_data->n_particles; + + if(diff == 0) + { + return(TNG_SUCCESS); + } + if(diff < 0) + { + printf("TNG library: Already more particles than requested implicit "); + printf("particle count.\n"); + printf("TNG library: Cannot set implicit particle count. %s: %d\n", + __FILE__, __LINE__); + } + + if(diff > 0) + { + stat = tng_molecule_find(tng_data, "TNG_IMPLICIT_MOL", -1, &mol); + if(stat != TNG_SUCCESS) + { + stat = tng_util_trajectory_molecule_add(tng_data, + "TNG_IMPLICIT_MOL", + diff, + &mol); + if(stat != TNG_SUCCESS) + { + return(stat); + } + stat = tng_molecule_chain_add(tng_data, mol, "", &chain); + if(stat != TNG_SUCCESS) + { + return(stat); + } + stat = tng_chain_residue_add(tng_data, chain, "", &res); + if(stat != TNG_SUCCESS) + { + return(stat); + } + tng_residue_atom_add(tng_data, res, "", "", &atom); + } + else + { + if(mol->n_atoms != 1) + { + n_mod = diff % mol->n_atoms; + if(n_mod != 0) + { + printf("TNG library: Number of atoms in implicit molecule "); + printf("not compatible with requested implicit particle cnt.\n"); + printf("TNG library: Cannot set implicit particle count. %s: %d\n", + __FILE__, __LINE__); + return(TNG_FAILURE); + } + diff /= mol->n_atoms; + } + tng_molecule_cnt_set(tng_data, mol, diff); + } + } return(TNG_SUCCESS); } @@ -9729,7 +9793,7 @@ 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 --;) { @@ -9743,20 +9807,20 @@ 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. + *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); } @@ -14399,7 +14463,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add tng_function_status stat; TNG_ASSERT(name, "TNG library: name must not be a NULL pointer"); - TNG_ASSERT(cnt>=0, "TNG library: cnt must be a positive integer"); + TNG_ASSERT(cnt>=0, "TNG library: cnt must be >= 0"); stat = tng_molecule_add(tng_data, name, mol); if(stat != TNG_SUCCESS) |