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 );
}
}
}
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
int start_j, end_j, hb_start_j, hb_end_j;
int hblist[MAX_BONDS];
int itr, top;
int num_hb_intrs = 0;
ivec rel_jk;
real r_ij, r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
real e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
rvec dvec_jk, force, ext_press;
// rtensor temp_rtensor, total_rtensor;
hbond_parameters *hbp;
bond_order_data *bo_ij;
bond_data *pbond_ij;
far_neighbor_data *nbr_jk;
reax_list *bonds, *hbonds;
bond_data *bond_list;
hbond_data *hbond_list;
// tally variables
real fi_tmp[3], fk_tmp[3], delij[3], delkj[3];
bonds = (*lists) + BONDS;
bond_list = bonds->select.bond_list;
hbonds = (*lists) + HBONDS;
hbond_list = hbonds->select.hbond_list;
/* loops below discover the Hydrogen bonds between i-j-k triplets.
here j is H atom and there has to be some bond between i and j.
Hydrogen bond is between j and k.
so in this function i->X, j->H, k->Z when we map
variables onto the ones in the handout.*/
for( j = 0; j < system->n; ++j )
/* j has to be of type H */
if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
/*set j's variables */
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds );
hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds );
top = 0;
for( pi = start_j; pi < end_j; ++pi ) {
pbond_ij = &( bond_list[pi] );
i = pbond_ij->nbr;
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
if( system->reax_param.sbp[type_i].p_hbond == 2 &&
bo_ij->BO >= HB_THRESHOLD )
hblist[top++] = pi;
}
// fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
// j, top, hb_start_j, hb_end_j );
for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
/* set k's varibles */
k = hbond_list[pk].nbr;
type_k = system->my_atoms[k].type;
nbr_jk = hbond_list[pk].ptr;
r_jk = nbr_jk->d;
rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
for( itr = 0; itr < top; ++itr ) {
pi = hblist[itr];
pbond_ij = &( bonds->select.bond_list[pi] );
i = pbond_ij->nbr;
if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
r_ij = pbond_ij->d;
hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
++num_hb_intrs;
Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&theta, &cos_theta );
/* the derivative of cos(theta) */
Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&dcos_theta_di, &dcos_theta_dj,
&dcos_theta_dk );
/* hyrogen bond energy*/
sin_theta2 = sin( theta/2.0 );
sin_xhz4 = SQR(sin_theta2);
sin_xhz4 *= sin_xhz4;
cos_xhz1 = ( 1.0 - cos_theta );
exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
r_jk / hbp->r0_hb - 2.0 ) );
data->my_en.e_hb += e_hb =
hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
CEhb3 = -hbp->p_hb3 *
(-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
/*fprintf( stdout,
"%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
system->my_atoms[k].orig_id,
r_jk, theta, hbp->p_hb1, exp_hb2, hbp->p_hb3, hbp->r0_hb,
exp_hb3, sin_xhz4, e_hb ); */
/* hydrogen bond forces */
bo_ij->Cdbo += CEhb1; // dbo term
if( control->virial == 0 ) {
// dcos terms
rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
}
else {
/* for pressure coupling, terms that are not related to bond order
derivatives are added directly into pressure vector/tensor */
rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
rvec_Scale( force, +CEhb2, dcos_theta_dk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_Scale( force, CEhb3/r_jk, dvec_jk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
}
/* tally into per-atom virials */
if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
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, CEhb2, dcos_theta_di);
rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
}
#ifdef TEST_ENERGY
/* fprintf( out_control->ehb,
"%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n%24.15e%24.15e%24.15e\n",
dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
fprintf( out_control->ehb, "%24.15e%24.15e%24.15e\n",
CEhb1, CEhb2, CEhb3 ); */
fprintf( out_control->ehb,
//"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
"%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
system->my_atoms[k].orig_id,
r_jk, theta, bo_ij->BO, e_hb, data->my_en.e_hb );
#endif
#ifdef TEST_FORCES
Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb ); //dbo term
// dcos terms
rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
// dr terms
rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk );
rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk );
#endif
}
}
}
}
#if defined(DEBUG)
fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs );
fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->my_en.e_hb );
fprintf( stderr, "hydbonds: ext_press (%24.15e %24.15e %24.15e)\n",
data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
}
void Hydrogen_Bonds( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, k, pi, pk;
int type_i, type_j, type_k;
int start_j, end_j, hb_start_j, hb_end_j;
int hblist[MAX_BONDS];
int itr, top;
int num_hb_intrs = 0;
ivec rel_jk;
real r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
real e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
rvec dvec_jk, force, ext_press;
hbond_parameters *hbp;
bond_order_data *bo_ij;
bond_data *pbond_ij;
far_neighbor_data *nbr_jk;
reax_list *bonds, *hbonds;
bond_data *bond_list;
hbond_data *hbond_list;
// tally variables
real fi_tmp[3], fk_tmp[3], delij[3], delkj[3];
bonds = (*lists) + BONDS;
bond_list = bonds->select.bond_list;
hbonds = (*lists) + HBONDS;
hbond_list = hbonds->select.hbond_list;
for( j = 0; j < system->n; ++j )
if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) {
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index( system->my_atoms[j].Hindex, hbonds );
hb_end_j = End_Index( system->my_atoms[j].Hindex, hbonds );
if (type_j < 0) continue;
top = 0;
for( pi = start_j; pi < end_j; ++pi ) {
pbond_ij = &( bond_list[pi] );
i = pbond_ij->nbr;
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
bo_ij = &(pbond_ij->bo_data);
if( system->reax_param.sbp[type_i].p_hbond == 2 &&
bo_ij->BO >= HB_THRESHOLD )
hblist[top++] = pi;
}
for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
/* set k's varibles */
k = hbond_list[pk].nbr;
type_k = system->my_atoms[k].type;
if (type_k < 0) continue;
nbr_jk = hbond_list[pk].ptr;
r_jk = nbr_jk->d;
rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
for( itr = 0; itr < top; ++itr ) {
pi = hblist[itr];
pbond_ij = &( bonds->select.bond_list[pi] );
i = pbond_ij->nbr;
if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) {
bo_ij = &(pbond_ij->bo_data);
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
hbp = &(system->reax_param.hbp[ type_i ][ type_j ][ type_k ]);
++num_hb_intrs;
Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&theta, &cos_theta );
/* the derivative of cos(theta) */
Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
&dcos_theta_di, &dcos_theta_dj,
&dcos_theta_dk );
/* hyrogen bond energy*/
sin_theta2 = sin( theta/2.0 );
sin_xhz4 = SQR(sin_theta2);
sin_xhz4 *= sin_xhz4;
cos_xhz1 = ( 1.0 - cos_theta );
exp_hb2 = exp( -hbp->p_hb2 * bo_ij->BO );
exp_hb3 = exp( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
r_jk / hbp->r0_hb - 2.0 ) );
data->my_en.e_hb += e_hb =
hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
CEhb2 = -hbp->p_hb1/2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
CEhb3 = -hbp->p_hb3 *
(-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
/* hydrogen bond forces */
bo_ij->Cdbo += CEhb1; // dbo term
if( control->virial == 0 ) {
// dcos terms
rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di );
rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
rvec_ScaledAdd( workspace->f[k], +CEhb2, dcos_theta_dk );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_ScaledAdd( workspace->f[k], +CEhb3/r_jk, dvec_jk );
}
else {
rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
rvec_Add( workspace->f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj );
ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
rvec_Scale( force, +CEhb2, dcos_theta_dk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
// dr terms
rvec_ScaledAdd( workspace->f[j], -CEhb3/r_jk, dvec_jk );
rvec_Scale( force, CEhb3/r_jk, dvec_jk );
rvec_Add( workspace->f[k], force );
rvec_iMultiply( ext_press, rel_jk, force );
rvec_ScaledAdd( data->my_ext_press, 1.0, ext_press );
}
/* tally into per-atom virials */
if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
rvec_ScaledSum( delij, 1., system->my_atoms[j].x,
-1., system->my_atoms[i].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[j].x,
-1., system->my_atoms[k].x );
rvec_Scale(fi_tmp, CEhb2, dcos_theta_di);
rvec_Scale(fk_tmp, CEhb2, dcos_theta_dk);
rvec_ScaledAdd(fk_tmp, CEhb3/r_jk, dvec_jk);
system->pair_ptr->ev_tally3(i,j,k,e_hb,0.0,fi_tmp,fk_tmp,delij,delkj);
}
}
}
}
}
}
