int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
comm = mpi_data->world;
//for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
//system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
// Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
num_nbrs = Estimate_NumNeighbors( system, lists );
if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
*lists+FAR_NBRS, comm )){
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated far_nbrs: num_far=%d, space=%dMB\n",
system->my_rank, num_nbrs,
(int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
Generate_Neighbor_Lists( system, data, workspace, lists );
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
workspace->L = NULL;
workspace->U = NULL;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
system->my_rank, Htop,
(int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS );
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#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 */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS );
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = MAX( num_3body*SAFE_ZONE, MIN_3BODIES );
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, *lists+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
int nrecv[MAX_NBRS];
MPI_Comm comm;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#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 */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*SAFE_ZONE, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, (*lists)+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
int Init_ListsOMP( reax_system *system, control_params *control,
simulation_data * /* data */, storage * /* workspace */,
reax_list **lists, mpi_datatypes *mpi_data, char * /* msg */)
{
int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if (control->hbond_cut > 0) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
int nthreads = control->nthreads;
reax_list *bonds = (*lists)+BONDS;
for (i = 0; i < bonds->num_intrs; ++i)
bonds->select.bond_list[i].bo_data.CdboReduction =
(double*) smalloc(sizeof(double)*nthreads, "CdboReduction", comm);
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
free( hb_top );
free( bond_top );
return SUCCESS;
}
