diff options
| -rw-r--r-- | include/tng_io.h | 259 | ||||
| -rw-r--r-- | src/tests/md_openmp_util.c | 6 |
2 files changed, 130 insertions, 135 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 66a550a..0bd15a0 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -68,13 +68,18 @@ * * Test by running: * - * bin/tng_testing + * bin/tests/tng_testing * * @section change_sec Change Log * * See git log for full revision history. * - * revs - Avoid memory allocation if no data is submitted when adding data + * revs + * - High-level API functions added (not for managing molecules yet) + * - Added functions for reading data blocks into 1D arrays. + * - TNG compression added. + * - C++ interface added. + * - Avoid memory allocation if no data is submitted when adding data * blocks. * - Added function tng_num_frames_per_frame_set_set * - Added data block IDs for charges, b-factors and occupancy. @@ -96,8 +101,7 @@ * * @section examples_sec Examples * - * There are some examples of how to use the library in the testing located - * located in src/tests/ + * There are some examples of how to use the library located in src/tests/ * * @subsection tng_subsec TNG files * @@ -105,133 +109,123 @@ * contains a very short example of a TNG file containing a few water molecules, * a box shape description and positions in 10 frames. * - * It is also possible to run the bin/md_openmp (see src/tests/md_openmp.c) + * It is also possible to run the bin/examples/md_openmp_util + * (see src/tests/md_openmp_util.c) * testing program, which will save MD simulations output to a new file * (saved in the example_files directory). * - * These files can be read using the bin/tng_io_read_pos testing program. + * These files can be read using the bin/examples/tng_io_read_pos_util + * program. * * @subsection c_subsec C * + * Example writing data to a TNG file (just an extract): + * \code + * for ( step = 1; step < step_num; step++ ) + * { + * compute ( np, nd, pos, vel, mass, force, &potential, &kinetic ); + * + * if(step % step_save == 0) + * { + * // Write positions, velocities and forces + * if(tng_util_pos_write(traj, step, pos) != TNG_SUCCESS) + * { + * printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + * break; + * } + * if(tng_util_vel_write(traj, step, vel) != TNG_SUCCESS) + * { + * printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + * break; + * } + * if(tng_util_force_write(traj, step, force) != TNG_SUCCESS) + * { + * printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + * break; + * } + * } + * update ( np, nd, pos, vel, force, acc, mass, dt ); + * } + * \endcode + * + * Example reading positions from a TNG file: * \code * #include <stdlib.h> * #include <stdio.h> * #include <tng_io.h> - * + * * int main(int argc, char **argv) * { * tng_trajectory_t traj; - * union data_values ***positions = 0; // A 3-dimensional array to be populated - * int64_t n_particles, n_values_per_frame, n_frames, tot_n_frames; - * tng_data_type data_type; - * int i, j; - * int64_t particle = 0; + * // Assume that the data is stored as floats. The data is placed in 1-D + * // arrays + * float *positions = 0, *box_shape = 0; + * int64_t n_particles, n_frames, tot_n_frames, stride_length, i, j; * // Set a default frame range - * int first_frame = 0, last_frame = 50; - * char atom_name[64], res_name[64], chain_name[64]; - * - * if(argc <= 1) - * { - * printf("No file specified\n"); - * printf("Usage:\n"); - * printf("tng_io_read_pos <tng_file> [particle number = %"PRId64"] " - * "[first_frame = %d] [last_frame = %d]\n", - * particle, first_frame, last_frame); - * exit(1); - * } - * + * int64_t first_frame = 0, last_frame = 5000; + * int k; + * * // A reference must be passed to allocate memory - * if(tng_trajectory_init(&traj) != TNG_SUCCESS) + * tng_util_trajectory_open(argv[1], 'r', &traj); + * + * if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS) * { - * tng_trajectory_destroy(&traj); + * printf("Cannot determine the number of frames in the file\n"); + * tng_util_trajectory_close(&traj); * exit(1); * } - * tng_input_file_set(traj, argv[1]); - * - * // Read the file headers - * tng_file_headers_read(traj, TNG_USE_HASH); - * - * if(argc >= 3) + * + * if(tng_num_particles_get(traj, &n_particles) != TNG_SUCCESS) * { - * particle = strtoll(argv[2], 0, 10); - * if(argc >= 4) - * { - * first_frame = strtoll(argv[3], 0, 10); - * if(argc >= 5) - * { - * last_frame = strtoll(argv[4], 0, 10); - * } - * } - * } - * - * if(tng_num_frames_get(traj, &tot_n_frames) != TNG_SUCCESS) - * { - * printf("Cannot determine the number of frames in the file\n"); - * tng_trajectory_destroy(&traj); + * printf("Cannot determine the number of particles in the file\n"); + * tng_util_trajectory_close(&traj); * exit(1); * } - * + * * printf("%"PRId64" frames in file\n", tot_n_frames); - * + * * if(last_frame > tot_n_frames - 1) * { * last_frame = tot_n_frames - 1; * } - * - * n_frames = last_frame - first_frame + 1; - * - * if(tng_atom_name_of_particle_nr_get(traj, particle, atom_name, - * sizeof(atom_name)) == - * TNG_SUCCESS && - * tng_residue_name_of_particle_nr_get(traj, particle, res_name, - * sizeof(res_name)) == - * TNG_SUCCESS && - * tng_chain_name_of_particle_nr_get(traj, particle, chain_name, - * sizeof(chain_name)) == - * TNG_SUCCESS) + * + * if(tng_util_box_shape_read(traj, &box_shape, &stride_length) == + * TNG_SUCCESS) * { - * printf("Particle: %s (%s: %s)\n", atom_name, chain_name, res_name); + * printf("Simulation box shape: "); + * for(i=0; i < 9; i++) + * { + * printf("%f ", box_shape[i]); + * } + * printf("\n"); * } * else * { - * printf("Particle name not found\n"); + * printf("Simulation box shape not set in the file (or could not be read)\n"); * } - * + * + * n_frames = last_frame - first_frame + 1; + * + * * // Get the positions of all particles in the requested frame range. * // The positions are stored in the positions array. * // N.B. No proper error checks. - * if(tng_particle_data_interval_get(traj, TNG_TRAJ_POSITIONS, first_frame, - * last_frame, TNG_USE_HASH, &positions, &n_particles, &n_values_per_frame, - * &data_type) == TNG_SUCCESS) + * if(tng_util_pos_read_range(traj, 0, last_frame, &positions, &stride_length) + * == TNG_SUCCESS) * { - * if(particle >= n_particles) + * // Print the positions of the wanted particle (zero based) + * for(i=0; i < n_frames; i += stride_length) * { - * printf("Chosen particle out of range. Only %"PRId64" particles in trajectory.\n", n_particles); - * } - * else - * { - * // Print the positions of the wanted particle (zero based) - * for(i=0; i<n_frames; i++) + * printf("\nFrame %"PRId64":\n", first_frame + i); + * for(j=0; j < n_particles; j++) * { - * printf("%d", first_frame + i); - * for(j=0; j<n_values_per_frame; j++) + * printf("Atom nr: %"PRId64"", j); + * for(k=0; k < 3; k++) * { - * switch(data_type) - * { - * case TNG_INT_DATA: - * printf("\t%"PRId64"", positions[i][particle][j].i); - * break; - * case TNG_FLOAT_DATA: - * printf("\t%f", positions[i][particle][j].f); - * break; - * case TNG_DOUBLE_DATA: - * printf("\t%f", positions[i][particle][j].d); - * break; - * default: - * break; - * } - * printf("\n"); + * printf("\t%f", positions[i/stride_length*n_particles* + * 3+j*3+k]); * } + * printf("\n"); * } * } * } @@ -239,15 +233,14 @@ * { * printf("Cannot read positions\n"); * } - * + * * // Free memory * if(positions) * { - * tng_particle_data_values_free(traj, positions, n_frames, n_particles, - * n_values_per_frame, data_type); + * free(positions); * } - * tng_trajectory_destroy(&traj); - * + * tng_util_trajectory_close(&traj); + * * return(0); * } * @@ -500,7 +493,9 @@ extern "C" #endif /** @defgroup group1 Low-level API - * These functions give high control of the TNG data management. + * These functions give detailed control of the TNG data management. Most + * things can be done using the more convenient high-level API functions + * instead. * @{ */ @@ -1912,7 +1907,7 @@ tng_function_status DECLSPECDLLEXPORT tng_time_get_str /** @defgroup group2 High-level API * These functions make it easier to access and output TNG data. They * are recommended unless there is a special reason to use the more - * detailed functions. + * detailed functions available in the low-level API. * @{ */ @@ -1941,39 +1936,39 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_open tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close (tng_trajectory_t *tng_data_p); -tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get - (tng_trajectory_t tng_data, - int64_t *n_mols, - int64_t *molecule_cnt_list, - tng_molecule_t *mols); - -tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add - (tng_trajectory_t tng_data, - const char *name, - const int64_t cnt, - tng_molecule_t *mol); - -tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get - (tng_trajectory_t tng_data, - const tng_molecule_t mol, - int64_t *n_particles, - char ***names, - char ***types, - char ***res_names, - int64_t **res_ids, - char ***chain_names, - int64_t **chain_ids); - -tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set - (tng_trajectory_t tng_data, - tng_molecule_t mol, - const int64_t n_particles, - const char **names, - const char **types, - const char **res_names, - const int64_t *res_ids, - const char **chain_names, - const int64_t *chain_ids); +// tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get +// (tng_trajectory_t tng_data, +// int64_t *n_mols, +// int64_t *molecule_cnt_list, +// tng_molecule_t *mols); +// +// tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecule_add +// (tng_trajectory_t tng_data, +// const char *name, +// const int64_t cnt, +// tng_molecule_t *mol); +// +// tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get +// (tng_trajectory_t tng_data, +// const tng_molecule_t mol, +// int64_t *n_particles, +// char ***names, +// char ***types, +// char ***res_names, +// int64_t **res_ids, +// char ***chain_names, +// int64_t **chain_ids); +// +// tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_set +// (tng_trajectory_t tng_data, +// tng_molecule_t mol, +// const int64_t n_particles, +// const char **names, +// const char **types, +// const char **res_names, +// const int64_t *res_ids, +// const char **chain_names, +// const int64_t *chain_ids); /** * @brief High-level function for reading the positions of all particles diff --git a/src/tests/md_openmp_util.c b/src/tests/md_openmp_util.c index 339e1bb..920c35d 100644 --- a/src/tests/md_openmp_util.c +++ b/src/tests/md_openmp_util.c @@ -269,17 +269,17 @@ int main ( int argc, char *argv[] ) if(tng_util_pos_write(traj, step, pos) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); - exit(1); + break; } if(tng_util_vel_write(traj, step, vel) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); - exit(1); + break; } if(tng_util_force_write(traj, step, force) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); - exit(1); + break; } } update ( np, nd, pos, vel, force, acc, mass, dt ); |