int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name,
MPI_Comm comm )
{
Deallocate_Matrix( *H );
if( !Allocate_Matrix( H, n, m, comm ) ) {
fprintf(stderr, "not enough space for %s matrix. terminating!\n", name);
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n", name, n, m );
fprintf( stderr, "memory allocated: %s = %dMB\n",
name, (int)(m * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
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;
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;
}
void Init_MatVec( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list *far_nbrs )
{
int i, fillin;
real s_tmp, t_tmp;
//char fname[100];
if(control->refactor > 0 &&
((data->step-data->prev_steps)%control->refactor==0 || workspace->L==NULL)){
//Print_Linear_System( system, control, workspace, data->step );
Sort_Matrix_Rows( workspace->H );
//fprintf( stderr, "H matrix sorted\n" );
Calculate_Droptol( workspace->H, workspace->droptol, control->droptol );
//fprintf( stderr, "drop tolerances calculated\n" );
if( workspace->L == NULL ) {
fillin = Estimate_LU_Fill( workspace->H, workspace->droptol );
if( Allocate_Matrix( &(workspace->L), far_nbrs->n, fillin ) == 0 ||
Allocate_Matrix( &(workspace->U), far_nbrs->n, fillin ) == 0 ){
fprintf( stderr, "not enough memory for LU matrices. terminating.\n" );
exit(INSUFFICIENT_SPACE);
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "fillin = %d\n", fillin );
fprintf( stderr, "allocated memory: L = U = %ldMB\n",
fillin * sizeof(sparse_matrix_entry) / (1024*1024) );
#endif
}
ICHOLT( workspace->H, workspace->droptol, workspace->L, workspace->U );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "icholt-" );
//sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
//Print_Sparse_Matrix2( workspace->L, fname );
//Print_Sparse_Matrix( U );
#endif
}
/* extrapolation for s & t */
for( i = 0; i < system->N; ++i ) {
// no extrapolation
//s_tmp = workspace->s[0][i];
//t_tmp = workspace->t[0][i];
// linear
//s_tmp = 2 * workspace->s[0][i] - workspace->s[1][i];
//t_tmp = 2 * workspace->t[0][i] - workspace->t[1][i];
// quadratic
//s_tmp = workspace->s[2][i] + 3 * (workspace->s[0][i]-workspace->s[1][i]);
t_tmp = workspace->t[2][i] + 3*(workspace->t[0][i]-workspace->t[1][i]);
// cubic
s_tmp = 4 * (workspace->s[0][i] + workspace->s[2][i]) -
(6 * workspace->s[1][i] + workspace->s[3][i] );
//t_tmp = 4 * (workspace->t[0][i] + workspace->t[2][i]) -
// (6 * workspace->t[1][i] + workspace->t[3][i] );
// 4th order
//s_tmp = 5 * (workspace->s[0][i] - workspace->s[3][i]) +
// 10 * (-workspace->s[1][i] + workspace->s[2][i] ) + workspace->s[4][i];
//t_tmp = 5 * (workspace->t[0][i] - workspace->t[3][i]) +
// 10 * (-workspace->t[1][i] + workspace->t[2][i] ) + workspace->t[4][i];
workspace->s[4][i] = workspace->s[3][i];
workspace->s[3][i] = workspace->s[2][i];
workspace->s[2][i] = workspace->s[1][i];
workspace->s[1][i] = workspace->s[0][i];
workspace->s[0][i] = s_tmp;
workspace->t[4][i] = workspace->t[3][i];
workspace->t[3][i] = workspace->t[2][i];
workspace->t[2][i] = workspace->t[1][i];
workspace->t[1][i] = workspace->t[0][i];
workspace->t[0][i] = t_tmp;
}
}
