diff options
| -rw-r--r-- | include/tng_io.h | 28 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 200 | ||||
| -rw-r--r-- | src/tests/md_openmp.c | 38 | ||||
| -rw-r--r-- | src/tests/md_openmp_util.c | 67 | ||||
| -rw-r--r-- | src/tests/tng_io_read_pos_util.c | 9 |
5 files changed, 300 insertions, 42 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index 1085d17..2e47e58 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1981,16 +1981,36 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_read_range float **box_shape, int64_t *stride_length); -tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequence_set +tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f, + const int64_t block_id, + const char *block_name, + const tng_compression compression); + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set (tng_trajectory_t tng_data, const int64_t f); -tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequence_set +tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set (tng_trajectory_t tng_data, const int64_t f); -tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequence_set - (tng_trajectory_t tng_data, const int64_t f); +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_frequency_set + (tng_trajectory_t tng_data, + const int64_t f); + +tng_function_status DECLSPECDLLEXPORT tng_util_generic_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *values, + const int64_t block_id, + const char *block_name, + const tng_compression compression); tng_function_status DECLSPECDLLEXPORT tng_util_pos_write (tng_trajectory_t tng_data, diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 3397fcd..e6b4d8c 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -3825,7 +3825,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, uncompressed_len, __FILE__, __LINE__); return(TNG_CRITICAL); } - + result = tng_compress_uncompress_float(start_pos, f_dest); } else @@ -4813,8 +4813,40 @@ static tng_function_status tng_particle_data_block_write } else if(data->values) { + + if(block->id == TNG_TRAJ_VELOCITIES) + { + for(i=0; i<n_frames / stride_length; i++) + { + printf("%d\n", i); + for(j=0; j<n_particles; j++) + { + printf("%d: %f %f %f %"PRId64"\n", j, *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3)), + *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3 +1)), + *(float *)(data->values + sizeof(float) * (i * n_particles * 3 + j * 3 +2)), + sizeof(float) * (i * n_particles * 3 + j * 3)); + } + } + } + memcpy(block->block_contents + offset, data->values, block->block_contents_size - offset); + + if(block->id == TNG_TRAJ_VELOCITIES) + { + for(i=0; i<n_frames / stride_length; i++) + { + printf("%d\n", i); + for(j=0; j<n_particles; j++) + { + printf("%d: %f %f %f %"PRId64"\n", j, *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3)), + *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3 +1)), + *(float *)(block->block_contents + offset + sizeof(float) * (i * n_particles * 3 + j * 3 +2)), + sizeof(float) * (i * n_particles * 3 + j * 3)); + } + } + } + switch(data->datatype) { case TNG_FLOAT_DATA: @@ -10085,6 +10117,13 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new frame_set = &tng_data->current_trajectory_frame_set; + curr_pos = ftell(tng_data->output_file); + + if(curr_pos <= 10) + { + tng_file_headers_write(tng_data, TNG_USE_HASH); + } + /* Set pointer to previous frame set to the one that was loaded * before. * FIXME: This is a bit risky. If they are not added in order @@ -10330,7 +10369,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add data->n_frames = n_frames; data->codec_id = codec_id; data->compression_multiplier = 1.0; - + switch(datatype) { case TNG_FLOAT_DATA: @@ -10463,7 +10502,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add /* FIXME: Memory leak from strings. */ data->strings = 0; } - + data->stride_length = tng_max(stride_length, 1); data->n_values_per_frame = n_values_per_frame; data->n_frames = n_frames; @@ -12883,7 +12922,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get last_frame_pos = tng_min(frame_set->first_frame + n_frames - *stride_length, end_frame_nr - frame_set->first_frame); - + memcpy(*values + (current_frame_pos - start_frame_nr) *frame_size / *stride_length, current_values, @@ -12960,7 +12999,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close frame_set->n_frames = frame_set->n_unwritten_frames; tng_frame_set_write(*tng_data_p, TNG_USE_HASH); } - + return(tng_trajectory_destroy(tng_data_p)); } @@ -13233,15 +13272,118 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_read_range return(stat); } -tng_function_status DECLSPECDLLEXPORT tng_util_pos_write +tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f, + const int64_t block_id, + const char *block_name, + const tng_compression compression) +{ + tng_trajectory_frame_set_t frame_set = &tng_data-> + current_trajectory_frame_set; + tng_particle_data_t data; + int64_t n_particles, n_frames = 10000; + tng_function_status stat; + + if(!frame_set || tng_data->n_trajectory_frame_sets <= 0) + { + stat = tng_frame_set_new(tng_data, 0, n_frames); + if(stat != TNG_SUCCESS) + { + printf("Cannot create frame set. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + } + else + { + n_frames = frame_set->n_frames; + } + + tng_num_particles_get(tng_data, &n_particles); + + if(tng_particle_data_find(tng_data, block_id, &data) + != TNG_SUCCESS) + { + stat = tng_particle_data_block_add(tng_data, block_id, + block_name, + TNG_FLOAT_DATA, + TNG_TRAJECTORY_BLOCK, + n_frames, 3, f, + 0, n_particles, + compression, 0); + if(stat != TNG_SUCCESS) + { + printf("Error adding positions data block. %s: %d\n", __FILE__, + __LINE__); + return(stat); + } + data = &frame_set->tr_particle_data[frame_set-> + n_particle_data_blocks - 1]; + stat = tng_allocate_particle_data_mem(tng_data, data, n_frames, + f, n_particles, + 3); + } + else + { + data->stride_length = f; + } + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f) +{ + return(tng_util_generic_write_frequency_set(tng_data, f, + TNG_TRAJ_POSITIONS, + "POSITIONS", + TNG_TNG_COMPRESSION)); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_vel_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f) +{ + return(tng_util_generic_write_frequency_set(tng_data, f, + TNG_TRAJ_VELOCITIES, + "VELOCITIES", + TNG_TNG_COMPRESSION)); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_force_write_frequency_set + (tng_trajectory_t tng_data, + const int64_t f) +{ + return(tng_util_generic_write_frequency_set(tng_data, f, + TNG_TRAJ_FORCES, + "FORCES", + TNG_GZIP_COMPRESSION)); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_frequency_set + (tng_trajectory_t tng_data, + const int64_t f) +{ + return(tng_util_generic_write_frequency_set(tng_data, f, + TNG_TRAJ_BOX_SHAPE, + "BOX SHAPE", + TNG_GZIP_COMPRESSION)); +} + +tng_function_status DECLSPECDLLEXPORT tng_util_generic_write (tng_trajectory_t tng_data, const int64_t frame_nr, - const float *positions) + const float *values, + const int64_t block_id, + const char *block_name, + const tng_compression compression) { tng_trajectory_frame_set_t frame_set = &tng_data-> current_trajectory_frame_set; tng_particle_data_t data; - int64_t n_particles, n_frames = 10000, stride_length = 100, frame_pos; + int64_t n_particles, n_frames = 10000, stride_length = 400, frame_pos; tng_function_status stat; if(!frame_set || tng_data->n_trajectory_frame_sets <= 0) @@ -13253,8 +13395,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write __LINE__); return(stat); } + frame_set->n_unwritten_frames = frame_nr - frame_set->first_frame + 1; } - if(frame_nr >= frame_set->first_frame + n_frames) + else if(frame_nr >= frame_set->first_frame + n_frames) { stat = tng_frame_set_write(tng_data, TNG_USE_HASH); if(stat != TNG_SUCCESS) @@ -13264,29 +13407,35 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write return(stat); } stat = tng_frame_set_new(tng_data, frame_set->first_frame + - n_frames, n_frames); + frame_set->n_frames, n_frames); if(stat != TNG_SUCCESS) { printf("Cannot create frame set. %s: %d\n", __FILE__, __LINE__); return(stat); } + frame_set->n_unwritten_frames = frame_nr - frame_set->first_frame + 1; + } + else + { + frame_set->n_unwritten_frames += stride_length; + n_frames = frame_set->n_frames; } frame_pos = (frame_nr - frame_set->first_frame) / stride_length; tng_num_particles_get(tng_data, &n_particles); - if(tng_particle_data_find(tng_data, TNG_TRAJ_POSITIONS, &data) + if(tng_particle_data_find(tng_data, block_id, &data) != TNG_SUCCESS) { - stat = tng_particle_data_block_add(tng_data, TNG_TRAJ_POSITIONS, - "POSITIONS", + stat = tng_particle_data_block_add(tng_data, block_id, + block_name, TNG_FLOAT_DATA, TNG_TRAJECTORY_BLOCK, n_frames, 3, stride_length, 0, n_particles, - TNG_TNG_COMPRESSION, 0); + compression, 0); if(stat != TNG_SUCCESS) { printf("Error adding positions data block. %s: %d\n", __FILE__, @@ -13299,19 +13448,33 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write stride_length, n_particles, 3); } + printf("frame nr: %"PRId64" first frame: %"PRId64" stride_length: %"PRId64" frame pos: %"PRId64"\n", + frame_nr, frame_set->first_frame, stride_length, frame_pos); + printf("pos: %"PRId64" length: %"PRId64"\n", sizeof(float) * frame_pos * n_particles * 3, sizeof(float) * n_particles * 3); memcpy(data->values + sizeof(float) * frame_pos * n_particles * 3, - positions, sizeof(float) * n_particles * 3); - - frame_set->n_unwritten_frames += stride_length; + values, sizeof(float) * n_particles * 3); return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_util_pos_write + (tng_trajectory_t tng_data, + const int64_t frame_nr, + const float *positions) +{ + return(tng_util_generic_write(tng_data, frame_nr, positions, + TNG_TRAJ_POSITIONS, "POSITIONS", + TNG_TNG_COMPRESSION)); +} + tng_function_status DECLSPECDLLEXPORT tng_util_vel_write (tng_trajectory_t tng_data, const int64_t frame_nr, const float *velocities) { + return(tng_util_generic_write(tng_data, frame_nr, velocities, + TNG_TRAJ_VELOCITIES, "VELOCITIES", + TNG_TNG_COMPRESSION)); } tng_function_status DECLSPECDLLEXPORT tng_util_force_write @@ -13319,6 +13482,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_force_write const int64_t frame_nr, const float *forces) { + return(tng_util_generic_write(tng_data, frame_nr, forces, + TNG_TRAJ_FORCES, "FORCES", + TNG_GZIP_COMPRESSION)); } diff --git a/src/tests/md_openmp.c b/src/tests/md_openmp.c index 108beb6..2314e6f 100644 --- a/src/tests/md_openmp.c +++ b/src/tests/md_openmp.c @@ -240,7 +240,7 @@ int main ( int argc, char *argv[] ) TNG_TRAJECTORY_BLOCK, n_frames_per_frame_set, 3, 1, 0, np, - TNG_TNG_COMPRESSION, + TNG_UNCOMPRESSED, 0) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); @@ -252,7 +252,7 @@ int main ( int argc, char *argv[] ) TNG_TRAJECTORY_BLOCK, n_frames_per_frame_set, 3, 1, 0, np, - TNG_TNG_COMPRESSION, + TNG_UNCOMPRESSED, 0) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); @@ -294,7 +294,39 @@ int main ( int argc, char *argv[] ) wtime = omp_get_wtime ( ); - for ( step = 1; step <= step_num; step++ ) + if(tng_frame_particle_data_write(traj, frames_saved_cnt, + TNG_TRAJ_POSITIONS, 0, np, + pos, TNG_USE_HASH) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + if(tng_frame_particle_data_write(traj, frames_saved_cnt, + TNG_TRAJ_VELOCITIES, 0, np, + vel, TNG_USE_HASH) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + if(tng_frame_particle_data_write(traj, frames_saved_cnt, + TNG_TRAJ_FORCES, 0, np, + force, TNG_USE_HASH) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + if(step % (step_save * sparse_save) == 0) + { + if(tng_frame_data_write(traj, frames_saved_cnt, 10101, &potential, + TNG_USE_HASH) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + } + frames_saved_cnt++; + + for ( step = 1; step < step_num; step++ ) { compute ( np, nd, pos, vel, mass, force, &potential, &kinetic ); diff --git a/src/tests/md_openmp_util.c b/src/tests/md_openmp_util.c index 6a2f377..99ab60e 100644 --- a/src/tests/md_openmp_util.c +++ b/src/tests/md_openmp_util.c @@ -155,17 +155,17 @@ int main ( int argc, char *argv[] ) /* Add the box shape data block and write the file headers */ - if(tng_data_block_add(traj, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_DOUBLE_DATA, - TNG_NON_TRAJECTORY_BLOCK, 1, 9, 1, TNG_UNCOMPRESSED, - box_shape) == TNG_CRITICAL || - tng_file_headers_write(traj, TNG_USE_HASH) == TNG_CRITICAL) - { - free(box_shape); - tng_util_trajectory_close(&traj); - printf(" Cannot write trajectory headers and box shape.\n"); - exit(1); - } - free(box_shape); +// if(tng_data_block_add(traj, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE", TNG_DOUBLE_DATA, +// TNG_NON_TRAJECTORY_BLOCK, 1, 9, 1, TNG_UNCOMPRESSED, +// box_shape) == TNG_CRITICAL || +// tng_file_headers_write(traj, TNG_USE_HASH) == TNG_CRITICAL) +// { +// free(box_shape); +// tng_util_trajectory_close(&traj); +// printf(" Cannot write trajectory headers and box shape.\n"); +// exit(1); +// } +// free(box_shape); printf ( "\n" ); printf ( " Initializing positions, velocities, and accelerations.\n" ); @@ -184,11 +184,11 @@ int main ( int argc, char *argv[] ) e0 = potential + kinetic; /* Saving frequency */ - step_save = 100; + step_save = 400; step_print = 0; step_print_index = 0; - step_print_num = 10; + step_print_num = 100; /* This is the main time stepping loop: @@ -214,15 +214,44 @@ int main ( int argc, char *argv[] ) step_print_index++; step_print = ( step_print_index * step_num ) / step_print_num; + if(tng_util_pos_write_frequency_set(traj, step_save) != TNG_SUCCESS) + { + printf("Error setting writing frequency data. %s: %d\n", + __FILE__, __LINE__); + exit(1); + } + if(tng_util_vel_write_frequency_set(traj, step_save) != TNG_SUCCESS) + { + printf("Error setting writing frequency data. %s: %d\n", + __FILE__, __LINE__); + exit(1); + } + if(tng_util_force_write_frequency_set(traj, step_save) != TNG_SUCCESS) + { + printf("Error setting writing frequency data. %s: %d\n", + __FILE__, __LINE__); + exit(1); + } + if(tng_util_pos_write(traj, 0, pos) != TNG_SUCCESS) { printf("Error adding data. %s: %d\n", __FILE__, __LINE__); exit(1); } + if(tng_util_vel_write(traj, 0, vel) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + if(tng_util_force_write(traj, 0, force) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } wtime = omp_get_wtime ( ); - for ( step = 1; step <= step_num; step++ ) + for ( step = 1; step < step_num; step++ ) { compute ( np, nd, pos, vel, mass, force, &potential, &kinetic ); @@ -240,6 +269,16 @@ int main ( int argc, char *argv[] ) printf("Error adding data. %s: %d\n", __FILE__, __LINE__); exit(1); } + if(tng_util_vel_write(traj, step, vel) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } + if(tng_util_force_write(traj, step, force) != TNG_SUCCESS) + { + printf("Error adding data. %s: %d\n", __FILE__, __LINE__); + exit(1); + } } update ( np, nd, pos, vel, force, acc, mass, dt ); } diff --git a/src/tests/tng_io_read_pos_util.c b/src/tests/tng_io_read_pos_util.c index 12bf2ed..322f4a4 100644 --- a/src/tests/tng_io_read_pos_util.c +++ b/src/tests/tng_io_read_pos_util.c @@ -22,8 +22,9 @@ int main(int argc, char **argv) { tng_trajectory_t traj; - float *positions = 0; // A 1-dimensional array - // to be populated + /* Assume that the data is stored as floats. The data is placed in 1-D + * arrays */ + float *positions = 0, *velocities = 0, *forces = 0; int64_t n_particles, n_frames, tot_n_frames, stride_length, i, j; // Set a default frame range int64_t first_frame = 0, last_frame = 5000; @@ -41,7 +42,7 @@ int main(int argc, char **argv) // A reference must be passed to allocate memory tng_util_trajectory_open(argv[1], 'r', &traj); - + if(argc >= 3) { first_frame = strtoll(argv[2], 0, 10); @@ -64,7 +65,7 @@ int main(int argc, char **argv) tng_util_trajectory_close(&traj); exit(1); } - + printf("%"PRId64" frames in file\n", tot_n_frames); if(last_frame > tot_n_frames - 1) |