void Init_Forces(reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace, list **lists,
output_controls *out_control) {
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 flag;
real r_ij, r2, self_coef;
real dr3gamij_1, dr3gamij_3, Tap;
//real val, dif, base;
real C12, C34, C56;
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
real BO, BO_s, BO_pi, BO_pi2;
real p_boc1, p_boc2;
sparse_matrix *H;
list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
//LR_lookup_table *t;
reax_atom *atom_i, *atom_j;
bond_data *ibond, *jbond;
bond_order_data *bo_ij, *bo_ji;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
H = workspace->H;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
p_boc1 = system->reaxprm.gp.l[0];
p_boc2 = system->reaxprm.gp.l[1];
for (i = 0; i < system->N; ++i) {
atom_i = &(system->atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
H->start[i] = Htop;
btop_i = End_Index(i, bonds);
sbp_i = &(system->reaxprm.sbp[type_i]);
ihb = ihb_top = -1;
if (control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1)
ihb_top = End_Index(workspace->hbond_index[i], hbonds);
for (pj = start_i; pj < end_i; ++pj) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
atom_j = &(system->atoms[j]);
flag = 0;
if ((data->step - data->prev_steps) % control->reneighbor == 0) {
if (nbr_pj->d <= control->r_cut)
flag = 1;
else
flag = 0;
} else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x,
&(system->box), nbr_pj->dvec)) <= SQR(control->r_cut)) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
if (flag) {
type_j = system->atoms[j].type;
r_ij = nbr_pj->d;
sbp_j = &(system->reaxprm.sbp[type_j]);
twbp = &(system->reaxprm.tbp[type_i][type_j]);
self_coef = (i == j) ? 0.5 : 1.0;
/* H matrix entry */
Tap = control->Tap7 * r_ij + control->Tap6;
Tap = Tap * r_ij + control->Tap5;
Tap = Tap * r_ij + control->Tap4;
Tap = Tap * r_ij + control->Tap3;
Tap = Tap * r_ij + control->Tap2;
Tap = Tap * r_ij + control->Tap1;
Tap = Tap * r_ij + control->Tap0;
dr3gamij_1 = (r_ij * r_ij * r_ij + twbp->gamma);
dr3gamij_3 = POW(dr3gamij_1, 0.33333333333333);
H->entries[Htop].j = j;
H->entries[Htop].val = self_coef * Tap * EV_to_KCALpMOL
/ dr3gamij_3;
++Htop;
/* hydrogen bond lists */
if (control->hb_cut > 0 && (ihb == 1 || ihb == 2) && nbr_pj->d
<= control->hb_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 (ihb == 2 && jhb == 1) {
jhb_top = End_Index(workspace->hbond_index[j], 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(workspace->hbond_index[j], jhb_top + 1,
hbonds);
++num_hbonds;
}
}
/* uncorrected bond orders */
if (far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut) {
r2 = SQR(r_ij);
if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
C12 = twbp->p_bo1 * POW(r_ij / twbp->r_s, twbp->p_bo2);
BO_s = (1.0 + control->bo_cut) * EXP(C12);
} else
BO_s = C12 = 0.0;
if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
C34 = twbp->p_bo3 * POW(r_ij / twbp->r_p, twbp->p_bo4);
BO_pi = EXP(C34);
} else
BO_pi = C34 = 0.0;
if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
C56 = twbp->p_bo5 * POW(r_ij / twbp->r_pp, twbp->p_bo6);
BO_pi2 = EXP(C56);
} else
BO_pi2 = C56 = 0.0;
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
if (BO >= control->bo_cut) {
num_bonds += 2;
/****** bonds i-j and j-i ******/
ibond = &(bonds->select.bond_list[btop_i]);
btop_j = End_Index(j, bonds);
jbond = &(bonds->select.bond_list[btop_j]);
ibond->nbr = j;
jbond->nbr = i;
ibond->d = r_ij;
jbond->d = r_ij;
rvec_Copy(ibond->dvec, nbr_pj->dvec);
rvec_Scale(jbond->dvec, -1, nbr_pj->dvec);
ivec_Copy(ibond->rel_box, nbr_pj->rel_box);
ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box);
ibond->dbond_index = btop_i;
jbond->dbond_index = btop_i;
ibond->sym_index = btop_j;
jbond->sym_index = btop_i;
++btop_i;
Set_End_Index(j, btop_j + 1, bonds);
bo_ij = &(ibond->bo_data);
bo_ji = &(jbond->bo_data);
bo_ji->BO = bo_ij->BO = BO;
bo_ji->BO_s = bo_ij->BO_s = BO_s;
bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
/* Bond Order page2-3, derivative of total bond order prime */
Cln_BOp_s = twbp->p_bo2 * C12 / r2;
Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
/* Only dln_BOp_xx wrt. dr_i is stored here, note that
dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s,
ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi
* Cln_BOp_pi, ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi2, -bo_ij->BO_pi2
* Cln_BOp_pi2, ibond->dvec);
rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi);
rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2);
/* Only dBOp wrt. dr_i is stored here, note that
dBOp/dr_i = -dBOp/dr_j and all others are 0 */
rvec_Scale(bo_ij->dBOp, -(bo_ij->BO_s * Cln_BOp_s
+ bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2
* Cln_BOp_pi2), ibond->dvec);
rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp);
rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
rvec_Add(workspace->dDeltap_self[j], bo_ji->dBOp);
bo_ij->BO_s -= control->bo_cut;
bo_ij->BO -= control->bo_cut;
bo_ji->BO_s -= control->bo_cut;
bo_ji->BO -= control->bo_cut;
workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
/*fprintf( stderr, "%d %d %g %g %g\n",
i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/
/*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
Cln_BOp_s, twbp->p_bo2, C12 );
fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
Cln_BOp_pi, twbp->p_bo4, C34 );
fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n",
Cln_BOp_pi2, twbp->p_bo6, C56 );*/
/*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2);
fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4);
fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6);
fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
twbp->r_s, twbp->r_p, twbp->r_pp );
fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/
/*fprintf( stderr, "\tfactors: %g %g %g\n",
-(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
bo_ij->BO_pi2 * Cln_BOp_pp),
-bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/
/*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] );
fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
bo_ij->dln_BOp_pi[2] );
fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n",
bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
bo_ij->dln_BOp_pi2[2] );*/
Set_End_Index(j, btop_j + 1, bonds);
}
}
}
}
H->entries[Htop].j = i;
H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
++Htop;
Set_End_Index(i, btop_i, bonds);
if (ihb == 1)
Set_End_Index(workspace->hbond_index[i], ihb_top, hbonds);
//fprintf( stderr, "%d bonds start: %d, end: %d\n",
// i, Start_Index( i, bonds ), End_Index( i, bonds ) );
}
// mark the end of j list
H->start[i] = Htop;
/* validate lists - decide if reallocation is required! */
Validate_Lists(workspace, lists, data->step, system->N, H->m, Htop,
num_bonds, num_hbonds);
#if defined(DEBUG_FOCUS)
fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
data->step, Htop, num_bonds, num_hbonds );
#endif
}
void Init_Forces_noQEq( 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 btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
double cutoff;
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
}
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 = MAX( control->hbond_cut, control->bond_cut );
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local && 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;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* 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;
}
}
}
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 && ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
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_Tab(reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace, list **lists,
output_controls *out_control) {
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 tmin, tmax, r;
int ihb, jhb, ihb_top, jhb_top;
int flag;
real r_ij, r2, self_coef;
real val, dif, base;
real C12, C34, C56;
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
real BO, BO_s, BO_pi, BO_pi2;
real p_boc1, p_boc2;
sparse_matrix *H;
list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
LR_lookup_table *t;
reax_atom *atom_i, *atom_j;
bond_data *ibond, *jbond;
bond_order_data *bo_ij, *bo_ji;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
H = workspace->H;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
p_boc1 = system->reaxprm.gp.l[0];
p_boc2 = system->reaxprm.gp.l[1];
for (i = 0; i < system->N; ++i) {
atom_i = &(system->atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
H->start[i] = Htop;
btop_i = End_Index(i, bonds);
sbp_i = &(system->reaxprm.sbp[type_i]);
ihb = ihb_top = -1;
if (control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1)
ihb_top = End_Index(workspace->hbond_index[i], hbonds);
for (pj = start_i; pj < end_i; ++pj) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
atom_j = &(system->atoms[j]);
flag = 0;
if ((data->step - data->prev_steps) % control->reneighbor == 0) {
if (nbr_pj->d <= control->r_cut)
flag = 1;
else
flag = 0;
} else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x,
&(system->box), nbr_pj->dvec)) <= SQR(control->r_cut)) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
if (flag) {
type_j = system->atoms[j].type;
r_ij = nbr_pj->d;
sbp_j = &(system->reaxprm.sbp[type_j]);
twbp = &(system->reaxprm.tbp[type_i][type_j]);
self_coef = (i == j) ? 0.5 : 1.0;
tmin = MIN( type_i, type_j );
tmax = MAX( type_i, type_j );
t = &(LR[tmin][tmax]);
/* cubic spline interpolation */
r = (int) (r_ij * t->inv_dx);
if (r == 0)
++r;
base = (real) (r + 1) * t->dx;
dif = r_ij - base;
val = ((t->ele[r].d * dif + t->ele[r].c) * dif + t->ele[r].b)
* dif + t->ele[r].a;
val *= EV_to_KCALpMOL / C_ele;
H->entries[Htop].j = j;
H->entries[Htop].val = self_coef * val;
++Htop;
/* hydrogen bond lists */
if (control->hb_cut > 0 && (ihb == 1 || ihb == 2) && nbr_pj->d
<= control->hb_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 (ihb == 2 && jhb == 1) {
jhb_top = End_Index(workspace->hbond_index[j], 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(workspace->hbond_index[j], jhb_top + 1,
hbonds);
++num_hbonds;
}
}
/* uncorrected bond orders */
if (far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut) {
r2 = SQR(r_ij);
if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
C12 = twbp->p_bo1 * POW(r_ij / twbp->r_s, twbp->p_bo2);
BO_s = (1.0 + control->bo_cut) * EXP(C12);
} else
BO_s = C12 = 0.0;
if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
C34 = twbp->p_bo3 * POW(r_ij / twbp->r_p, twbp->p_bo4);
BO_pi = EXP(C34);
} else
BO_pi = C34 = 0.0;
if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
C56 = twbp->p_bo5 * POW(r_ij / twbp->r_pp, twbp->p_bo6);
BO_pi2 = EXP(C56);
} else
BO_pi2 = C56 = 0.0;
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
if (BO >= control->bo_cut) {
num_bonds += 2;
/****** bonds i-j and j-i ******/
ibond = &(bonds->select.bond_list[btop_i]);
btop_j = End_Index(j, bonds);
jbond = &(bonds->select.bond_list[btop_j]);
ibond->nbr = j;
jbond->nbr = i;
ibond->d = r_ij;
jbond->d = r_ij;
rvec_Copy(ibond->dvec, nbr_pj->dvec);
rvec_Scale(jbond->dvec, -1, nbr_pj->dvec);
ivec_Copy(ibond->rel_box, nbr_pj->rel_box);
ivec_Scale(jbond->rel_box, -1, nbr_pj->rel_box);
ibond->dbond_index = btop_i;
jbond->dbond_index = btop_i;
ibond->sym_index = btop_j;
jbond->sym_index = btop_i;
++btop_i;
Set_End_Index(j, btop_j + 1, bonds);
bo_ij = &(ibond->bo_data);
bo_ji = &(jbond->bo_data);
bo_ji->BO = bo_ij->BO = BO;
bo_ji->BO_s = bo_ij->BO_s = BO_s;
bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
/* Bond Order page2-3, derivative of total bond order prime */
Cln_BOp_s = twbp->p_bo2 * C12 / r2;
Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
/* Only dln_BOp_xx wrt. dr_i is stored here, note that
dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s,
ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi
* Cln_BOp_pi, ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi2, -bo_ij->BO_pi2
* Cln_BOp_pi2, ibond->dvec);
rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi);
rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2);
/* Only dBOp wrt. dr_i is stored here, note that
dBOp/dr_i = -dBOp/dr_j and all others are 0 */
rvec_Scale(bo_ij->dBOp, -(bo_ij->BO_s * Cln_BOp_s
+ bo_ij->BO_pi * Cln_BOp_pi + bo_ij->BO_pi2
* Cln_BOp_pi2), ibond->dvec);
rvec_Scale(bo_ji->dBOp, -1., bo_ij->dBOp);
rvec_Add(workspace->dDeltap_self[i], bo_ij->dBOp);
rvec_Add(workspace->dDeltap_self[j], bo_ji->dBOp);
bo_ij->BO_s -= control->bo_cut;
bo_ij->BO -= control->bo_cut;
bo_ji->BO_s -= control->bo_cut;
bo_ji->BO -= control->bo_cut;
workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
Set_End_Index(j, btop_j + 1, bonds);
}
}
}
}
H->entries[Htop].j = i;
H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
++Htop;
Set_End_Index(i, btop_i, bonds);
if (ihb == 1)
Set_End_Index(workspace->hbond_index[i], ihb_top, hbonds);
}
// mark the end of j list
H->start[i] = Htop;
/* validate lists - decide if reallocation is required! */
Validate_Lists(workspace, lists, data->step, system->N, H->m, Htop,
num_bonds, num_hbonds);
#if defined(DEBUG_FOCUS)
fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
data->step, Htop, num_bonds, num_hbonds );
//Print_Bonds( system, bonds, "sbonds.out" );
//Print_Bond_List2( system, bonds, "sbonds.out" );
//Print_Sparse_Matrix2( H, "H.out" );
#endif
}
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 );
}
