void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control, MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int Htop, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
double r_ij, cutoff;
sparse_matrix *H;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for( i = system->n; i < system->N; ++i ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
}
H = workspace->H;
H->n = system->n;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local ) {
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
if( control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if( renbr ) {
if(nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ){
type_j = atom_j->type;
if (type_j < 0) continue;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* H matrix entry */
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
H->entries[Htop].j = j;
if( control->tabulate == 0 )
H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
++Htop;
}
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
}
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local ) {
H->end[i] = Htop;
if( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control, MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int Htop, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
real r_ij, cutoff;
sparse_matrix *H;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for( i = system->n; i < system->N; ++i ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
//workspace->done_after[i] = Start_Index( i, far_nbrs );
}
H = workspace->H;
H->n = system->n;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local ) {
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
if( control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
//fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
// j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
if( renbr ) {
if(nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ){
type_j = atom_j->type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* H matrix entry */
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
H->entries[Htop].j = j;
//fprintf( stdout, "%d%d %d %d\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id) );
if( control->tabulate == 0 )
H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
++Htop;
}
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//if( workspace->bond_mark[i] == 1000 )
// workspace->done_after[i] = pj;
}
//fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local ) {
H->end[i] = Htop;
if( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
//fprintf( stderr, "after the first init loop\n" );
/*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
Set_End_Index(i, start_i, bonds );
}*/
/*for( i = system->n; i < system->N; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = workspace->done_after[i];
if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
}
}*/
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
system->my_rank, data->step, Htop, num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
#if defined( DEBUG )
Print_Bonds( system, bonds, "debugbonds.out" );
Print_Bond_List2( system, bonds, "pbonds.out" );
Print_Sparse_Matrix( system, H );
for( i = 0; i < H->n; ++i )
for( j = H->start[i]; j < H->end[i]; ++j )
fprintf( stderr, "%d %d %.15e\n",
MIN(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
MAX(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
H->entries[j].val );
#endif
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
