Changed name from trg to tng

1 files changed, 0 insertions, 341 deletions

diff --git a/src/tests/trg_io_testing.c b/src/tests/trg_io_testing.c
deleted file mode 100644
index 08a2b90..0000000
--- a/src/tests/trg_io_testing.c
+++ /dev/null
@@ -1,341 +0,0 @@
-#include <inttypes.h>
-#include <stdlib.h>
-#include <string.h>
-#include "trg_io.h"
-
-
-
-
-static trg_function_status trg_setup_test_molecules(struct trg_trajectory *traj)
-{
-    struct trg_molecule *molecule;
-    struct trg_chain *chain;
-    struct trg_residue *residue;
-    struct trg_atom *atom;
-    int64_t cnt;
-//     int i;
-
-    trg_add_molecule(traj, "water", &molecule);
-    trg_add_chain_to_molecule(traj, molecule, "W", &chain);
-    trg_add_residue_to_chain(traj, chain, "WAT", &residue);
-    if(trg_add_atom_to_residue(traj, residue, "O", "O", &atom) == TRG_CRITICAL)
-    {
-        return(TRG_CRITICAL);
-    }
-    if(trg_add_atom_to_residue(traj, residue, "HO1", "H", &atom) == TRG_CRITICAL)
-    {
-        return(TRG_CRITICAL);
-    }
-    if(trg_add_atom_to_residue(traj, residue, "HO2", "H", &atom) == TRG_CRITICAL)
-    {
-        return(TRG_CRITICAL);
-    }
-    trg_set_molecule_cnt(traj, molecule, 200);
-    trg_get_molecule_cnt(traj, molecule, &cnt);
-    printf("Created %"PRId64" %s molecules.\n", cnt, molecule->name);
-//     traj->molecule_cnt_list[traj->n_molecules-1] = 5;
-//     trg_set_molecule_name(traj, &traj->molecules[1], "ligand");
-//     trg_set_molecule_name(traj, &traj->molecules[2], "water");
-//     trg_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(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom1", "type1") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom2", "type1") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom3", "type1") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom4", "type2") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom5", "type2") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom6", "type2") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[0], "atom7", "type3") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[1], "C1", "C") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[1], "O1", "O") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[1], "H11", "H") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[1], "H12", "H") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-//     if(trg_add_atom_to_molecule(traj, &traj->molecules[1], "H13", "H") == TRG_CRITICAL)
-//     {
-//         return(TRG_CRITICAL);
-//     }
-
-    return(TRG_SUCCESS);
-}
-
-static trg_function_status trg_test_read_and_write_file
-                (struct trg_trajectory *traj)
-{
-    trg_function_status stat;
-
-    stat = trg_read_file_headers(traj, TRG_KEEP_FILE_OPEN);
-    if(stat == TRG_CRITICAL)
-    {
-        return(stat);
-    }
-    stat = trg_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 = trg_read_next_frame_set(traj, TRG_KEEP_FILE_OPEN);
-        if(stat == TRG_CRITICAL)
-        {
-            return(stat);
-        }
-        stat = trg_write_frame_set(traj, TRG_KEEP_FILE_OPEN);
-    }
-    
-    return(stat);
-}
-
-static trg_function_status trg_test_write_and_read_traj(struct trg_trajectory *traj)
-{
-    int i, j, k, nr, tot_n_mols, cnt;
-    float *data, *molpos;
-    trg_function_status stat;
-    
-    /* Create molecules */
-    if(trg_setup_test_molecules(traj) == TRG_CRITICAL)
-    {
-        return(TRG_CRITICAL);
-    }
-
-    if(trg_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(trg_set_block_name(traj,
-                          &traj->non_trajectory_blocks[traj->n_non_trajectory_blocks++],
-                          "MOLECULES") == TRG_CRITICAL)
-    {
-        return(TRG_CRITICAL);
-    }
-
-    if(trg_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(trg_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(trg_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(trg_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);
-        }
-    }
-
-//     trg_add_ids_names_pair(traj, TRG_TRAJ_VELOCITIES, "BOX SHAPE");
-//     trg_add_ids_names_pair(traj, TRG_TRAJ_POSITIONS, "TRAJECTORY POSITIONS");
-//     trg_add_ids_names_pair(traj, TRG_TRAJ_VELOCITIES, "TRAJECTORY VELOCITIES");
-//     trg_add_ids_names_pair(traj, TRG_TRAJ_FORCES, "TRAJECTORY FORCES");
-//     trg_add_ids_names_pair(traj, 11000, "TEST DATA");
-        
-    free(molpos);
-    free(data);
-
-    trg_destroy_trajectory(traj);
-    trg_set_input_file(traj, "/tmp/trg_test.trg");
-    
-    stat = trg_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 = trg_read_next_frame_set(traj, TRG_KEEP_FILE_OPEN);
-        if(stat == TRG_CRITICAL)
-        {
-            return(stat);
-        }
-    }
-
-    return(stat);
-}
-
-int main()
-{
-    struct trg_trajectory traj;
-    char time_str[TRG_MAX_DATE_STR_LEN];
-    
-    if(trg_init_trajectory(&traj) != TRG_SUCCESS)
-    {
-        trg_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");
-
-    trg_get_time_str(&traj, time_str);
-
-    printf("Creation time: %s\n", time_str);
-    
-    trg_set_input_file(&traj, "trg_example.trg");
-    trg_set_output_file(&traj, "/tmp/trg_example_test.trg");
-
-//     if(trg_test_endianness(&traj) != TRG_SUCCESS)
-//     {
-//         printf("Test failed: Endianness. %s: %d\n", __FILE__, __LINE__);
-//     }
-
-    if(trg_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(trg_destroy_trajectory(&traj) == TRG_CRITICAL ||
-       trg_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");
-    }
-    
-
-    trg_set_output_file(&traj, "/tmp/trg_test.trg");
-    
-    if(trg_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(trg_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