/************* system *************/
inline void reax_atom_Copy( reax_atom *dest, reax_atom *src )
{
dest->orig_id = src->orig_id;
dest->type = src->type;
strcpy( dest->name, src->name );
rvec_Copy( dest->x, src->x );
rvec_Copy( dest->v, src->v );
rvec_Copy( dest->f_old, src->f_old );
rvec_Copy( dest->s, src->s );
rvec_Copy( dest->t, src->t );
dest->Hindex = src->Hindex;
dest->num_bonds = src->num_bonds;
dest->num_hbonds = src->num_hbonds;
}
void Copy_Positions( reax_system *system, static_storage *workspace )
{
int i;
for( i = 0; i < system->N; ++i )
rvec_Copy( workspace->x_old[i], system->atoms[i].x );
}
/* this version of Compute_Total_Force computes forces from
coefficients accumulated by all interaction functions.
Saves enormous time & space! */
void Compute_Total_Force( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, mpi_datatypes *mpi_data )
{
int i, pj;
reax_list *bonds = (*lists) + BONDS;
for( i = 0; i < system->N; ++i )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
if( i < bonds->select.bond_list[pj].nbr ) {
if( control->virial == 0 )
Add_dBond_to_Forces( system, i, pj, workspace, lists );
else
Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists );
}
//Print_Total_Force( system, data, workspace );
#if defined(PURE_REAX)
/* now all forces are computed to their partially-final values
based on the neighbors information each processor has had.
final values of force on each atom needs to be computed by adding up
all partially-final pieces */
Coll( system, mpi_data, workspace->f, mpi_data->mpi_rvec,
sizeof(rvec)/sizeof(void), rvec_unpacker );
for( i = 0; i < system->n; ++i )
rvec_Copy( system->my_atoms[i].f, workspace->f[i] );
#if defined(TEST_FORCES)
Coll( system, mpi_data, workspace->f_ele, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_vdw, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_be, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_lp, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_ov, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_un, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_ang, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_coa, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_pen, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_hb, mpi_data->mpi_rvec, rvec_unpacker );
Coll( system, mpi_data, workspace->f_tor, mpi_data->mpi_rvec, rvec_unpacker);
Coll( system, mpi_data, workspace->f_con, mpi_data->mpi_rvec, rvec_unpacker);
#endif
#endif
}
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_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 Valence_Angles( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
int start_j, end_j, start_pk, end_pk;
int cnt, num_thb_intrs;
double temp, temp_bo_jt, pBOjt7;
double p_val1, p_val2, p_val3, p_val4, p_val5;
double p_val6, p_val7, p_val8, p_val9, p_val10;
double p_pen1, p_pen2, p_pen3, p_pen4;
double p_coa1, p_coa2, p_coa3, p_coa4;
double trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk;
double exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2;
double dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj;
double CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8;
double CEpen1, CEpen2, CEpen3;
double e_ang, e_coa, e_pen;
double CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5;
double Cf7ij, Cf7jk, Cf8j, Cf9j;
double f7_ij, f7_jk, f8_Dj, f9_Dj;
double Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta;
double BOA_ij, BOA_jk;
rvec force, ext_press;
// Tallying variables
double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];
double delij[3], delkj[3];
three_body_header *thbh;
three_body_parameters *thbp;
three_body_interaction_data *p_ijk, *p_kji;
bond_data *pbond_ij, *pbond_jk, *pbond_jt;
bond_order_data *bo_ij, *bo_jk, *bo_jt;
reax_list *bonds = (*lists) + BONDS;
reax_list *thb_intrs = (*lists) + THREE_BODIES;
/* global parameters used in these calculations */
p_val6 = system->reax_param.gp.l[14];
p_val8 = system->reax_param.gp.l[33];
p_val9 = system->reax_param.gp.l[16];
p_val10 = system->reax_param.gp.l[17];
num_thb_intrs = 0;
for( j = 0; j < system->N; ++j ) { // Ray: the first one with system->N
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
p_val3 = system->reax_param.sbp[ type_j ].p_val3;
p_val5 = system->reax_param.sbp[ type_j ].p_val5;
SBOp = 0, prod_SBO = 1;
for( t = start_j; t < end_j; ++t ) {
bo_jt = &(bonds->select.bond_list[t].bo_data);
SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2);
temp = SQR( bo_jt->BO );
temp *= temp;
temp *= temp;
prod_SBO *= exp( -temp );
}
if( workspace->vlpex[j] >= 0 ){
vlpadj = 0;
dSBO2 = prod_SBO - 1;
}
else{
vlpadj = workspace->nlp[j];
dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]);
}
SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj);
dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj );
if( SBO <= 0 )
SBO2 = 0, CSBO2 = 0;
else if( SBO > 0 && SBO <= 1 ) {
SBO2 = pow( SBO, p_val9 );
CSBO2 = p_val9 * pow( SBO, p_val9 - 1 );
}
else if( SBO > 1 && SBO < 2 ) {
SBO2 = 2 - pow( 2-SBO, p_val9 );
CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 );
}
else
SBO2 = 2, CSBO2 = 0;
expval6 = exp( p_val6 * workspace->Delta_boc[j] );
for( pi = start_j; pi < end_j; ++pi ) {
Set_Start_Index( pi, num_thb_intrs, thb_intrs );
pbond_ij = &(bonds->select.bond_list[pi]);
bo_ij = &(pbond_ij->bo_data);
BOA_ij = bo_ij->BO - control->thb_cut;
if( BOA_ij/*bo_ij->BO*/ > 0.0 &&
( j < system->n || pbond_ij->nbr < system->n ) ) {
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
for( pk = start_j; pk < pi; ++pk ) {
start_pk = Start_Index( pk, thb_intrs );
end_pk = End_Index( pk, thb_intrs );
for( t = start_pk; t < end_pk; ++t )
if( thb_intrs->select.three_body_list[t].thb == i ) {
p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] );
p_kji = &(thb_intrs->select.three_body_list[t]);
p_ijk->thb = bonds->select.bond_list[pk].nbr;
p_ijk->pthb = pk;
p_ijk->theta = p_kji->theta;
rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
++num_thb_intrs;
break;
}
}
for( pk = pi+1; pk < end_j; ++pk ) {
pbond_jk = &(bonds->select.bond_list[pk]);
bo_jk = &(pbond_jk->bo_data);
BOA_jk = bo_jk->BO - control->thb_cut;
k = pbond_jk->nbr;
type_k = system->my_atoms[k].type;
p_ijk = &( thb_intrs->select.three_body_list[num_thb_intrs] );
Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&theta, &cos_theta );
Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d,
pbond_jk->dvec, pbond_jk->d,
&(p_ijk->dcos_di), &(p_ijk->dcos_dj),
&(p_ijk->dcos_dk) );
p_ijk->thb = k;
p_ijk->pthb = pk;
p_ijk->theta = theta;
sin_theta = sin( theta );
if( sin_theta < 1.0e-5 )
sin_theta = 1.0e-5;
++num_thb_intrs;
if( (j < system->n) && (BOA_jk > 0.0) &&
(bo_ij->BO > control->thb_cut) &&
(bo_jk->BO > control->thb_cut) &&
(bo_ij->BO * bo_jk->BO > control->thb_cutsq) ) {
thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] );
for( cnt = 0; cnt < thbh->cnt; ++cnt ) {
if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
thbp = &( thbh->prm[cnt] );
/* ANGLE ENERGY */
p_val1 = thbp->p_val1;
p_val2 = thbp->p_val2;
p_val4 = thbp->p_val4;
p_val7 = thbp->p_val7;
theta_00 = thbp->theta_00;
exp3ij = exp( -p_val3 * pow( BOA_ij, p_val4 ) );
f7_ij = 1.0 - exp3ij;
Cf7ij = p_val3 * p_val4 * pow( BOA_ij, p_val4 - 1.0 ) * exp3ij;
exp3jk = exp( -p_val3 * pow( BOA_jk, p_val4 ) );
f7_jk = 1.0 - exp3jk;
Cf7jk = p_val3 * p_val4 * pow( BOA_jk, p_val4 - 1.0 ) * exp3jk;
expval7 = exp( -p_val7 * workspace->Delta_boc[j] );
trm8 = 1.0 + expval6 + expval7;
f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
( p_val6 * expval6 * trm8 -
(2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7 ) );
theta_0 = 180.0 - theta_00 * (1.0 -
exp(-p_val10 * (2.0 - SBO2)));
theta_0 = DEG2RAD( theta_0 );
expval2theta = exp( -p_val2 * SQR(theta_0 - theta) );
if( p_val1 >= 0 )
expval12theta = p_val1 * (1.0 - expval2theta);
else // To avoid linear Me-H-Me angles (6/6/06)
expval12theta = p_val1 * -expval2theta;
CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
expval2theta * (theta_0 - theta);
Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
exp( -p_val10 * (2.0 - SBO2) );
CEval5 = -CEval4 * Ctheta_0 * CSBO2;
CEval6 = CEval5 * dSBO1;
CEval7 = CEval5 * dSBO2;
CEval8 = -CEval4 / sin_theta;
data->my_en.e_ang += e_ang =
f7_ij * f7_jk * f8_Dj * expval12theta;
/* END ANGLE ENERGY*/
/* PENALTY ENERGY */
p_pen1 = thbp->p_pen1;
p_pen2 = system->reax_param.gp.l[19];
p_pen3 = system->reax_param.gp.l[20];
p_pen4 = system->reax_param.gp.l[21];
exp_pen2ij = exp( -p_pen2 * SQR( BOA_ij - 2.0 ) );
exp_pen2jk = exp( -p_pen2 * SQR( BOA_jk - 2.0 ) );
exp_pen3 = exp( -p_pen3 * workspace->Delta[j] );
exp_pen4 = exp( p_pen4 * workspace->Delta[j] );
trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
Cf9j = ( -p_pen3 * exp_pen3 * trm_pen34 -
(2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 +
p_pen4 * exp_pen4 ) ) /
SQR( trm_pen34 );
data->my_en.e_pen += e_pen =
p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
CEpen1 = e_pen * Cf9j / f9_Dj;
temp = -2.0 * p_pen2 * e_pen;
CEpen2 = temp * (BOA_ij - 2.0);
CEpen3 = temp * (BOA_jk - 2.0);
/* END PENALTY ENERGY */
/* COALITION ENERGY */
p_coa1 = thbp->p_coa1;
p_coa2 = system->reax_param.gp.l[2];
p_coa3 = system->reax_param.gp.l[38];
p_coa4 = system->reax_param.gp.l[30];
exp_coa2 = exp( p_coa2 * workspace->Delta_val[j] );
data->my_en.e_coa += e_coa =
p_coa1 / (1. + exp_coa2) *
exp( -p_coa3 * SQR(workspace->total_bond_order[i]-BOA_ij) ) *
exp( -p_coa3 * SQR(workspace->total_bond_order[k]-BOA_jk) ) *
exp( -p_coa4 * SQR(BOA_ij - 1.5) ) *
exp( -p_coa4 * SQR(BOA_jk - 1.5) );
CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
CEcoa4 = -2 * p_coa3 *
(workspace->total_bond_order[i]-BOA_ij) * e_coa;
CEcoa5 = -2 * p_coa3 *
(workspace->total_bond_order[k]-BOA_jk) * e_coa;
/* END COALITION ENERGY */
/* FORCES */
bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
workspace->CdDelta[i] += CEcoa4;
workspace->CdDelta[k] += CEcoa5;
for( t = start_j; t < end_j; ++t ) {
pbond_jt = &( bonds->select.bond_list[t] );
bo_jt = &(pbond_jt->bo_data);
temp_bo_jt = bo_jt->BO;
temp = CUBE( temp_bo_jt );
pBOjt7 = temp * temp * temp_bo_jt;
bo_jt->Cdbo += (CEval6 * pBOjt7);
bo_jt->Cdbopi += CEval5;
bo_jt->Cdbopi2 += CEval5;
}
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di );
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk );
}
else {
rvec_Scale( force, CEval8, p_ijk->dcos_di );
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj );
rvec_Scale( force, CEval8, p_ijk->dcos_dk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
rvec_Add( data->my_ext_press, ext_press );
}
/* tally into per-atom virials */
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
/* Acquire vectors */
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,
-1., system->my_atoms[j].x );
rvec_Scale( fi_tmp, -CEval8, p_ijk->dcos_di );
rvec_Scale( fj_tmp, -CEval8, p_ijk->dcos_dj );
rvec_Scale( fk_tmp, -CEval8, p_ijk->dcos_dk );
eng_tmp = e_ang + e_pen + e_coa;
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
if( system->pair_ptr->vflag_atom)
system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj);
}
}
}
}
}
}
Set_End_Index(pi, num_thb_intrs, thb_intrs );
}
}
if( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE ) {
workspace->realloc.num_3body = num_thb_intrs;
if( num_thb_intrs > thb_intrs->num_intrs ) {
fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d",
data->step, num_thb_intrs, thb_intrs->num_intrs );
MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY );
}
}
}
int BOp( storage *workspace, reax_list *bonds, double bo_cut,
int i, int btop_i, far_neighbor_data *nbr_pj,
single_body_parameters *sbp_i, single_body_parameters *sbp_j,
two_body_parameters *twbp ) {
int j, btop_j;
double r2, C12, C34, C56;
double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
double BO, BO_s, BO_pi, BO_pi2;
bond_data *ibond, *jbond;
bond_order_data *bo_ij, *bo_ji;
j = nbr_pj->nbr;
r2 = SQR(nbr_pj->d);
if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + 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( nbr_pj->d / 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( nbr_pj->d / 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 >= bo_cut ) {
/****** 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 = nbr_pj->d;
jbond->d = nbr_pj->d;
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;
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 );
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 -= bo_cut;
bo_ij->BO -= bo_cut;
bo_ji->BO_s -= bo_cut;
bo_ji->BO -= 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;
return 1;
}
return 0;
}