init_md.c

        //THIS IS COMMENTED OUT - CHANGE ORIGINAL
        //Cuda_Init_HBond_Indices (hb_top, system->N);
        //THIS IS COMMENTED OUT - CHANGE ORIGINAL
        /****/

#if defined(DEBUG_FOCUS)
        fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
                system->my_rank, total_hbonds,
                (int)(total_hbonds * sizeof(hbond_data) / (1024 * 1024)) );
#endif
    }

    /* bonds list */
    Dev_Make_List( system->total_cap, system->total_bonds, TYP_BOND, *dev_lists + BONDS );
    Make_List( system->total_cap, system->total_bonds, TYP_BOND, *lists + BONDS );

    Cuda_Init_Bond_Indices( system );

#if defined(DEBUG_FOCUS)
    fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
            system->my_rank, total_bonds,
            (int)(total_bonds * sizeof(bond_data) / (1024 * 1024)) );
#endif

    /* 3bodies list: since a more accurate estimate of the num.
     * of three body interactions requires that bond orders have
     * been computed, delay estimation until for computation */

    sfree( hb_top, "Cuda_Init_Lists::hb_top" );

    return SUCCESS;
}
#endif


#if defined(PURE_REAX)
void Initialize( reax_system *system, control_params *control,
        simulation_data *data, storage *workspace,
        reax_list **lists, output_controls *out_control,
        mpi_datatypes *mpi_data )
{

    host_scratch = (void *)malloc( HOST_SCRATCH_SIZE );

    char msg[MAX_STR];

    if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
                 system->my_rank );
        fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
#endif

    if ( Init_System(system, control, data, workspace, mpi_data, msg) == FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: system initialized\n", system->my_rank );
#endif

    Init_Simulation_Data( system, control, data, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif

    Init_Workspace( system, control, workspace, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif

    if ( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
            FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif

    if ( Init_Output_Files(system, control, out_control, mpi_data, msg) == FAILURE)
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: could not open output files! terminating...\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: output files opened\n", system->my_rank );
#endif

    if ( control->tabulate )
    {
        if ( Init_Lookup_Tables(system, control, workspace->Tap, mpi_data, msg) == FAILURE )
        {
            fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
            fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
                     system->my_rank );
            MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
        }

#if defined(DEBUG)
        fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
#endif
    }

    Init_Force_Functions( control );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif

    /*#ifdef TEST_FORCES
      Init_Force_Test_Functions();
      fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
      #endif */
}


void Pure_Initialize( reax_system *system, control_params *control,
        simulation_data *data, storage *workspace,
        reax_list **lists, output_controls *out_control,
        mpi_datatypes *mpi_data )
{
    char msg[MAX_STR];

    Init_Simulation_Data( system, control, data, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif
    fprintf( stderr, "p%d: pure initialized simulation data\n", system->my_rank );

    Init_Workspace( system, control, workspace, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
    fprintf( stderr, "p%d: pure initialized workspace\n", system->my_rank );

    if ( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
            FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }
#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif
    fprintf( stderr, "p%d: pure initialized lists done \n", system->my_rank );

    Init_Force_Functions( control );
}


#ifdef HAVE_CUDA
void Cuda_Initialize( reax_system *system, control_params *control,
        simulation_data *data, storage *workspace,
        reax_list **lists, output_controls *out_control,
        mpi_datatypes *mpi_data )
{
    char msg[MAX_STR];
    real t_start, t_end;

    /* HOST/DEVICE SCRATCH */
    Cuda_Init_ScratchArea( );

    /* MPI_DATATYPES */
    if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
                 system->my_rank );
        fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }
    fprintf( stderr, "  [INIT MPI DATATYPES]\n" );

    /* SYSTEM */
    if ( Cuda_Init_System( system, control, data, workspace, mpi_data, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }
    fprintf( stderr, "  [CUDA INIT SYSTEM]\n" );

    /* GRID */
    dev_alloc_grid( system );
    Sync_Grid( &system->my_grid, &system->d_my_grid );
    fprintf( stderr, "  [DEV ALLOC GRID]\n" );

    //validate_grid( system );

    /* SIMULATION_DATA */
    Cuda_Init_Simulation_Data( system, control, data, msg );
    fprintf( stderr, "  [CUDA INIT SIMULATION DATA]\n" );

    /* WORKSPACE */
    Cuda_Init_Workspace( system, control, workspace, msg );
    fprintf( stderr, "  [CUDA INIT WORKSPACE]\n" );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif

    //Sync the taper here from host to device.

    /* CONTROL */
    dev_alloc_control( control );
    fprintf( stderr, "  [DEV ALLOC CONTROL]\n" );

    /* LISTS */
    if ( Cuda_Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
            FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }
    fprintf( stderr, "  [CUDA INIT LISTS]\n" );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif

    /* OUTPUT Files */
    if ( Init_Output_Files( system, control, out_control, mpi_data, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: could not open output files! terminating...\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }
    fprintf( stderr, "  [INIT OUTPUT FILES]\n" );

#if defined(DEBUG)
    fprintf( stderr, "p%d: output files opened\n", system->my_rank );
#endif

    /* Lookup Tables */
    if ( control->tabulate )
    {
        if ( Init_Lookup_Tables( system, control, dev_workspace->Tap, mpi_data, msg ) == FAILURE )
        {
            fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
            fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
                     system->my_rank );
            MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
        }
        fprintf( stderr, "  [INIT LOOKUP TABLES]\n" );

#if defined(DEBUG)
        fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
#endif
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: Device Initialization Done \n", system->my_rank );
#endif
}
#endif


#elif defined(LAMMPS_REAX)
void Initialize( reax_system *system, control_params *control,
                 simulation_data *data, storage *workspace,
                 reax_list **lists, output_controls *out_control,
                 mpi_datatypes *mpi_data )
{
    char msg[MAX_STR];

    host_scratch = (void *)malloc( HOST_SCRATCH_SIZE );

    if ( Init_System(system, msg) == FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: system initialized\n", system->my_rank );
#endif

    Init_Simulation_Data( system, control, data, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif

    Init_Workspace( system, control, workspace, msg );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif

    if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
                 system->my_rank );
        fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
#endif

    if ( Init_Lists( system, control, workspace, lists, msg ) == FAILURE )
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif

    if ( Init_Output_Files(system, control, out_control, mpi_data, msg) == FAILURE)
    {
        fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
        fprintf( stderr, "p%d: could not open output files! terminating...\n",
                 system->my_rank );
        MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
    }

#if defined(DEBUG)
    fprintf( stderr, "p%d: output files opened\n", system->my_rank );
#endif

    if ( control->tabulate )
    {
        if ( Init_Lookup_Tables( system, control, workspace->Tap, mpi_data, msg ) == FAILURE )
        {
            fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
            fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
                     system->my_rank );
            MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
        }

#if defined(DEBUG)
        fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
#endif
    }

    Init_Force_Functions( );

#if defined(DEBUG)
    fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif

    /*#if defined(TEST_FORCES)
      Init_Force_Test_Functions();
      fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
#endif*/
    }
#endif