Changed name from trg to tng

1 files changed, 341 insertions, 0 deletions

diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c
new file mode 100644
index 0000000..85a7294
--- /dev/null
+++ b/src/tests/tng_io_testing.c
@@ -0,0 +1,341 @@
+#include <inttypes.h>
+#include <stdlib.h>
+#include <string.h>
+#include "tng_io.h"
+
+
+
+
+static tng_function_status tng_setup_test_molecules(struct tng_trajectory *traj)
+{
+    struct tng_molecule *molecule;
+    struct tng_chain *chain;
+    struct tng_residue *residue;
+    struct tng_atom *atom;
+    int64_t cnt;
+//     int i;
+
+    tng_add_molecule(traj, "water", &molecule);
+    tng_add_chain_to_molecule(traj, molecule, "W", &chain);
+    tng_add_residue_to_chain(traj, chain, "WAT", &residue);
+    if(tng_add_atom_to_residue(traj, residue, "O", "O", &atom) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+    if(tng_add_atom_to_residue(traj, residue, "HO1", "H", &atom) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+    if(tng_add_atom_to_residue(traj, residue, "HO2", "H", &atom) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+    tng_set_molecule_cnt(traj, molecule, 200);
+    tng_get_molecule_cnt(traj, molecule, &cnt);
+    printf("Created %"PRId64" %s molecules.\n", cnt, molecule->name);
+//     traj->molecule_cnt_list[traj->n_molecules-1] = 5;
+//     tng_set_molecule_name(traj, &traj->molecules[1], "ligand");
+//     tng_set_molecule_name(traj, &traj->molecules[2], "water");
+//     tng_set_molecule_name(traj, &traj->molecules[3], "dummy");
+//     traj->molecules[0].id = 0;
+//     traj->molecules[1].id = 1;
+//     traj->molecules[2].id = 2;
+//     traj->molecules[3].id = 3;
+
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom1", "type1") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom2", "type1") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom3", "type1") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom4", "type2") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom5", "type2") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom6", "type2") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[0], "atom7", "type3") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[1], "C1", "C") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[1], "O1", "O") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[1], "H11", "H") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[1], "H12", "H") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+//     if(tng_add_atom_to_molecule(traj, &traj->molecules[1], "H13", "H") == TRG_CRITICAL)
+//     {
+//         return(TRG_CRITICAL);
+//     }
+
+    return(TRG_SUCCESS);
+}
+
+static tng_function_status tng_test_read_and_write_file
+                (struct tng_trajectory *traj)
+{
+    tng_function_status stat;
+
+    stat = tng_read_file_headers(traj, TRG_KEEP_FILE_OPEN);
+    if(stat == TRG_CRITICAL)
+    {
+        return(stat);
+    }
+    stat = tng_write_file_headers(traj, TRG_KEEP_FILE_OPEN);
+    if(stat == TRG_CRITICAL)
+    {
+        return(stat);
+    }
+
+    while(stat != TRG_CRITICAL && traj->input_file_pos < traj->input_file_len &&
+          traj->current_trajectory_frame_set.next_frame_set_file_pos != -1UL)
+    {
+        stat = tng_read_next_frame_set(traj, TRG_KEEP_FILE_OPEN);
+        if(stat == TRG_CRITICAL)
+        {
+            return(stat);
+        }
+        stat = tng_write_frame_set(traj, TRG_KEEP_FILE_OPEN);
+    }
+    
+    return(stat);
+}
+
+static tng_function_status tng_test_write_and_read_traj(struct tng_trajectory *traj)
+{
+    int i, j, k, nr, tot_n_mols, cnt;
+    float *data, *molpos;
+    tng_function_status stat;
+    
+    /* Create molecules */
+    if(tng_setup_test_molecules(traj) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+
+    if(tng_init_block(&traj->non_trajectory_blocks[traj->n_non_trajectory_blocks]) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+    traj->non_trajectory_blocks[traj->n_non_trajectory_blocks].id = TRG_MOLECULES;
+    if(tng_set_block_name(traj,
+                          &traj->non_trajectory_blocks[traj->n_non_trajectory_blocks++],
+                          "MOLECULES") == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+
+    if(tng_write_file_headers(traj, TRG_KEEP_FILE_OPEN) == TRG_CRITICAL)
+    {
+        return(TRG_CRITICAL);
+    }
+    
+    data = malloc(sizeof(float) * traj->n_particles *
+                  traj->frame_set_n_frames * 3);
+    if(!data)
+    {
+        printf("Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
+        return(TRG_CRITICAL);
+    }
+
+    tot_n_mols = 0;
+    for(i = 0; i < traj->n_molecules; i++)
+    {
+        tot_n_mols += traj->molecule_cnt_list[i];
+    }
+    molpos = malloc(sizeof(float) * tot_n_mols * 3);
+
+    /* Set initial coordinates */
+    for(i = 0; i < tot_n_mols; i++)
+    {
+        nr = i * 3;
+        /* Somewhat random coordinates (between 0 and 100),
+        * but not specifying a random seed */
+        molpos[nr] = 100.0 * rand() / (RAND_MAX + 1.0);
+        molpos[nr+1] = 100.0 * rand() / (RAND_MAX + 1.0);
+        molpos[nr+2] = 100.0 * rand() / (RAND_MAX + 1.0);
+    }
+
+    /* Generate 200 frame sets - each with 100 frames (by default) */
+    for(i = 0; i < 200; i++)
+    {
+        cnt = 0;
+        for(j = 0; j < traj->frame_set_n_frames; j++)
+        {
+            for(k = 0; k < tot_n_mols; k++)
+            {
+                nr = k * 3;
+                /* Move -1 to 1 */
+                molpos[nr] += 2 * (rand() / (RAND_MAX + 1.0)) - 1;
+                molpos[nr+1] += 2 * (rand() / (RAND_MAX + 1.0)) - 1;
+                molpos[nr+2] += 2 * (rand() / (RAND_MAX + 1.0)) - 1;
+
+                data[cnt++] = molpos[nr];
+                data[cnt++] = molpos[nr + 1];
+                data[cnt++] = molpos[nr + 2];
+                data[cnt++] = molpos[nr] + 1;
+                data[cnt++] = molpos[nr + 1] + 1;
+                data[cnt++] = molpos[nr + 2] + 1;
+                data[cnt++] = molpos[nr] - 1;
+                data[cnt++] = molpos[nr + 1] - 1;
+                data[cnt++] = molpos[nr + 2] - 1;
+            }
+        }
+        if(tng_new_frame_set(traj, i * traj->frame_set_n_frames,
+            traj->frame_set_n_frames) != TRG_SUCCESS)
+        {
+            printf("Error creating frame set %d. %s: %d\n",
+                   i, __FILE__, __LINE__);
+            free(molpos);
+            free(data);
+            return(TRG_CRITICAL);
+        }
+
+        if(tng_add_particle_data_block(traj, TRG_TRAJ_POSITIONS,
+                                       "POSITIONS",
+                                       TRG_FLOAT_DATA,
+                                       traj->frame_set_n_frames, 3,
+                                       1, 0, traj->n_particles,
+                                       TRG_UNCOMPRESSED,
+                                       data) != TRG_SUCCESS)
+        {
+            printf("Error adding data. %s: %d\n", __FILE__, __LINE__);
+            free(molpos);
+            free(data);
+            return(TRG_CRITICAL);
+        }
+        if(tng_write_frame_set(traj, TRG_KEEP_FILE_OPEN) != TRG_SUCCESS)
+        {
+            printf("Error writing frame set. %s: %d\n", __FILE__, __LINE__);
+            free(molpos);
+            free(data);
+            return(TRG_CRITICAL);
+        }
+    }
+
+//     tng_add_ids_names_pair(traj, TRG_TRAJ_VELOCITIES, "BOX SHAPE");
+//     tng_add_ids_names_pair(traj, TRG_TRAJ_POSITIONS, "TRAJECTORY POSITIONS");
+//     tng_add_ids_names_pair(traj, TRG_TRAJ_VELOCITIES, "TRAJECTORY VELOCITIES");
+//     tng_add_ids_names_pair(traj, TRG_TRAJ_FORCES, "TRAJECTORY FORCES");
+//     tng_add_ids_names_pair(traj, 11000, "TEST DATA");
+        
+    free(molpos);
+    free(data);
+
+    tng_destroy_trajectory(traj);
+    tng_set_input_file(traj, "/tmp/tng_test.tng");
+    
+    stat = tng_read_file_headers(traj, TRG_KEEP_FILE_OPEN);
+    
+    while(stat != TRG_CRITICAL && traj->input_file_pos < traj->input_file_len &&
+          traj->current_trajectory_frame_set.next_frame_set_file_pos != -1ULL)
+    {
+        stat = tng_read_next_frame_set(traj, TRG_KEEP_FILE_OPEN);
+        if(stat == TRG_CRITICAL)
+        {
+            return(stat);
+        }
+    }
+
+    return(stat);
+}
+
+int main()
+{
+    struct tng_trajectory traj;
+    char time_str[TRG_MAX_DATE_STR_LEN];
+    
+    if(tng_init_trajectory(&traj) != TRG_SUCCESS)
+    {
+        tng_destroy_trajectory(&traj);
+        printf("Test Init trajectory:\t\t\t\tFailed. %s: %d.\n",
+               __FILE__, __LINE__);
+        exit(1);
+    }
+    printf("Test Init trajectory:\t\t\t\tSucceeded.\n");
+
+    tng_get_time_str(&traj, time_str);
+
+    printf("Creation time: %s\n", time_str);
+    
+    tng_set_input_file(&traj, "tng_example.tng");
+    tng_set_output_file(&traj, "/tmp/tng_example_test.tng");
+
+//     if(tng_test_endianness(&traj) != TRG_SUCCESS)
+//     {
+//         printf("Test failed: Endianness. %s: %d\n", __FILE__, __LINE__);
+//     }
+
+    if(tng_test_read_and_write_file(&traj) == TRG_CRITICAL)
+    {
+        printf("Test Read and write file:\t\t\tFailed. %s: %d\n",
+               __FILE__, __LINE__);
+    }
+    else
+    {
+        printf("Test Read and write file:\t\t\tSucceeded.\n");
+    }
+    
+    if(tng_destroy_trajectory(&traj) == TRG_CRITICAL ||
+       tng_init_trajectory(&traj) == TRG_CRITICAL)
+    {
+        printf("Test Destroy and init trajectory:\t\tFailed. %s: %d\n",
+               __FILE__, __LINE__);
+    }
+    else
+    {
+        printf("Test Destroy and init trajectory:\t\tSucceeded.\n");
+    }
+    
+
+    tng_set_output_file(&traj, "/tmp/tng_test.tng");
+    
+    if(tng_test_write_and_read_traj(&traj) == TRG_CRITICAL)
+    {
+        printf("Test Write and read file:\t\t\tFailed. %s: %d\n",
+               __FILE__, __LINE__);
+    }
+    else
+    {
+        printf("Test Write and read file:\t\t\tSucceeded.\n");
+    }
+    
+    if(tng_destroy_trajectory(&traj) == TRG_CRITICAL)
+    {
+        printf("Test Destroy trajectory:\t\t\tFailed. %s: %d.\n",
+               __FILE__, __LINE__);
+        exit(1);
+    }
+    else
+    {
+        printf("Test Destroy trajectory:\t\t\tSucceeded.\n");
+    }
+    
+
+    printf("Tests finished\n");
+    
+    exit(0);
+}
\ No newline at end of file