Improved utility functions. Bug fixes.

3 files changed, 93 insertions, 21 deletions

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)