void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, pj, natoms;
int start_i, end_i, orig_i, orig_j;
real p_vdW1, p_vdW1i;
real powr_vdW1, powgi_vdW1;
real tmp, r_ij, fn13, exp1, exp2;
real Tap, dTap, dfn13, CEvd, CEclmb, de_core;
real dr3gamij_1, dr3gamij_3;
real e_ele, e_vdW, e_core;
rvec temp, ext_press;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_list *far_nbrs;
// rtensor temp_rtensor, total_rtensor;
natoms = system->n;
far_nbrs = (*lists) + FAR_NBRS;
p_vdW1 = system->reax_param.gp.l[28];
p_vdW1i = 1.0 / p_vdW1;
e_core = 0;
e_vdW = 0;
for( i = 0; i < natoms; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
orig_i = system->my_atoms[i].orig_id;
//fprintf( stderr, "i:%d, start_i: %d, end_i: %d\n", i, start_i, end_i );
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
orig_j = system->my_atoms[j].orig_id;
if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
r_ij = nbr_pj->d;
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
[ system->my_atoms[j].type ]);
/* Calculate Taper and its derivative */
// Tap = nbr_pj->Tap; -- precomputed during compte_H
Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
Tap = Tap * r_ij + workspace->Tap[5];
Tap = Tap * r_ij + workspace->Tap[4];
Tap = Tap * r_ij + workspace->Tap[3];
Tap = Tap * r_ij + workspace->Tap[2];
Tap = Tap * r_ij + workspace->Tap[1];
Tap = Tap * r_ij + workspace->Tap[0];
dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
dTap = dTap * r_ij + 5*workspace->Tap[5];
dTap = dTap * r_ij + 4*workspace->Tap[4];
dTap = dTap * r_ij + 3*workspace->Tap[3];
dTap = dTap * r_ij + 2*workspace->Tap[2];
dTap += workspace->Tap[1]/r_ij;
/*vdWaals Calculations*/
if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
{ // shielding
powr_vdW1 = pow(r_ij, p_vdW1);
powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
data->my_en.e_vdW += Tap * e_vdW;
dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
pow(r_ij, p_vdW1 - 2.0);
CEvd = dTap * e_vdW -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
}
else{ // no shielding
exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
data->my_en.e_vdW += Tap * e_vdW;
CEvd = dTap * e_vdW -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
{ // innner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
data->my_en.e_vdW += Tap * e_core;
de_core = -(twbp->acore/twbp->rcore) * e_core;
CEvd += dTap * e_core + Tap * de_core / r_ij;
}
/*Coulomb Calculations*/
dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
tmp = Tap / dr3gamij_3;
data->my_en.e_ele += e_ele =
C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
// fprintf( fout, "%5d %5d %10.6f %10.6f\n",
// MIN( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
// MAX( system->my_atoms[i].orig_id, system->my_atoms[j].orig_id ),
// CEvd, CEclmb );
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { /* NPT, iNPT or sNPT */
/* for pressure coupling, terms not related to bond order
derivatives are added directly into pressure vector/tensor */
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[i], -1., temp );
rvec_Add( workspace->f[j], temp );
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
// fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)
// force(%f %f %f) ext_press (%12.6f %12.6f %12.6f)\n",
// i, j, nbr_pj->rel_box[0], nbr_pj->rel_box[1], nbr_pj->rel_box[2],
// temp[0], temp[1], temp[2],
// data->ext_press[0], data->ext_press[1], data->ext_press[2] );
}
#ifdef TEST_ENERGY
// fprintf( out_control->evdw,
// "%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f%12.9f\n",
// workspace->Tap[7],workspace->Tap[6],workspace->Tap[5],
// workspace->Tap[4],workspace->Tap[3],workspace->Tap[2],
// workspace->Tap[1], Tap );
//fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
r_ij, e_vdW, data->my_en.e_vdW );
//fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
fprintf( out_control->ecou, "%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,
r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
e_ele, data->my_en.e_ele );
#endif
#ifdef TEST_FORCES
rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
#endif
}
}
}
#if defined(DEBUG)
fprintf( stderr, "nonbonded: ext_press (%12.6f %12.6f %12.6f)\n",
data->ext_press[0], data->ext_press[1], data->ext_press[2] );
MPI_Barrier( MPI_COMM_WORLD );
#endif
Compute_Polarization_Energy( system, data );
}
void vdW_Coulomb_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control )
{
int i, j, pj, natoms;
int start_i, end_i, flag;
rc_tagint orig_i, orig_j;
double p_vdW1, p_vdW1i;
double powr_vdW1, powgi_vdW1;
double tmp, r_ij, fn13, exp1, exp2;
double Tap, dTap, dfn13, CEvd, CEclmb, de_core;
double dr3gamij_1, dr3gamij_3;
double e_ele, e_vdW, e_core, SMALL = 0.0001;
double e_lg, de_lg, r_ij5, r_ij6, re6;
rvec temp, ext_press;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_list *far_nbrs;
// Tallying variables:
double pe_vdw, f_tmp, delij[3];
natoms = system->n;
far_nbrs = (*lists) + FAR_NBRS;
p_vdW1 = system->reax_param.gp.l[28];
p_vdW1i = 1.0 / p_vdW1;
e_core = 0;
e_vdW = 0;
e_lg = de_lg = 0.0;
for( i = 0; i < natoms; ++i ) {
if (system->my_atoms[i].type < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
orig_i = system->my_atoms[i].orig_id;
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
if (system->my_atoms[j].type < 0) continue;
orig_j = system->my_atoms[j].orig_id;
flag = 0;
if(nbr_pj->d <= control->nonb_cut) {
if (j < natoms) flag = 1;
else if (orig_i < orig_j) flag = 1;
else if (orig_i == orig_j) {
if (nbr_pj->dvec[2] > SMALL) flag = 1;
else if (fabs(nbr_pj->dvec[2]) < SMALL) {
if (nbr_pj->dvec[1] > SMALL) flag = 1;
else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
flag = 1;
}
}
}
if (flag) {
r_ij = nbr_pj->d;
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
[ system->my_atoms[j].type ]);
Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
Tap = Tap * r_ij + workspace->Tap[5];
Tap = Tap * r_ij + workspace->Tap[4];
Tap = Tap * r_ij + workspace->Tap[3];
Tap = Tap * r_ij + workspace->Tap[2];
Tap = Tap * r_ij + workspace->Tap[1];
Tap = Tap * r_ij + workspace->Tap[0];
dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
dTap = dTap * r_ij + 5*workspace->Tap[5];
dTap = dTap * r_ij + 4*workspace->Tap[4];
dTap = dTap * r_ij + 3*workspace->Tap[3];
dTap = dTap * r_ij + 2*workspace->Tap[2];
dTap += workspace->Tap[1]/r_ij;
/*vdWaals Calculations*/
if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
{ // shielding
powr_vdW1 = pow(r_ij, p_vdW1);
powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);
fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
data->my_en.e_vdW += Tap * e_vdW;
dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
pow(r_ij, p_vdW1 - 2.0);
CEvd = dTap * e_vdW -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
}
else{ // no shielding
exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
e_vdW = twbp->D * (exp1 - 2.0 * exp2);
data->my_en.e_vdW += Tap * e_vdW;
CEvd = dTap * e_vdW -
Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
}
if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
{ // innner wall
e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
data->my_en.e_vdW += Tap * e_core;
de_core = -(twbp->acore/twbp->rcore) * e_core;
CEvd += dTap * e_core + Tap * de_core / r_ij;
// lg correction, only if lgvdw is yes
if (control->lgflag) {
r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
data->my_en.e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
CEvd += dTap * e_lg + Tap * de_lg / r_ij;
}
}
/*Coulomb Calculations*/
dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );
tmp = Tap / dr3gamij_3;
data->my_en.e_ele += e_ele =
C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;
CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
pe_vdw = Tap * (e_vdW + e_core + e_lg);
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
f_tmp = -(CEvd + CEclmb);
system->pair_ptr->ev_tally(i,j,natoms,1,pe_vdw,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { /* NPT, iNPT or sNPT */
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[i], -1., temp );
rvec_Add( workspace->f[j], temp );
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
}
}
}
Compute_Polarization_Energy( system, data );
}
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
output_controls *out_control )
{
int i, j, pj, r, natoms, steps, update_freq, update_energies;
int type_i, type_j, tmin, tmax;
int start_i, end_i, orig_i, orig_j;
real r_ij, base, dif;
real e_vdW, e_ele;
real CEvd, CEclmb;
rvec temp, ext_press;
far_neighbor_data *nbr_pj;
reax_list *far_nbrs;
LR_lookup_table *t;
natoms = system->n;
far_nbrs = (*lists) + FAR_NBRS;
steps = data->step - data->prev_steps;
update_freq = out_control->energy_update_freq;
update_energies = update_freq > 0 && steps % update_freq == 0;
e_ele = e_vdW = 0;
for( i = 0; i < natoms; ++i ) {
type_i = system->my_atoms[i].type;
start_i = Start_Index(i,far_nbrs);
end_i = End_Index(i,far_nbrs);
orig_i = system->my_atoms[i].orig_id;
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
orig_j = system->my_atoms[j].orig_id;
if( nbr_pj->d <= control->nonb_cut && (j < natoms || orig_i < orig_j) ) {
j = nbr_pj->nbr;
type_j = system->my_atoms[j].type;
r_ij = nbr_pj->d;
tmin = MIN( type_i, type_j );
tmax = MAX( type_i, type_j );
t = &( LR[tmin][tmax] );
//t = &( LR[type_i][type_j] );
/* Cubic Spline Interpolation */
r = (int)(r_ij * t->inv_dx);
if( r == 0 ) ++r;
base = (real)(r+1) * t->dx;
dif = r_ij - base;
//fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif);
if( update_energies ) {
e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
t->vdW[r].a;
e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
t->ele[r].a;
e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
data->my_en.e_vdW += e_vdW;
data->my_en.e_ele += e_ele;
}
CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
t->CEvd[r].a;
CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
t->CEclmb[r].a;
CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { // NPT, iNPT or sNPT
/* for pressure coupling, terms not related to bond order derivatives
are added directly into pressure vector/tensor */
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[i], -1., temp );
rvec_Add( workspace->f[j], temp );
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
#ifdef TEST_ENERGY
//fprintf( out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->evdw, "%6d%6d%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
r_ij, e_vdW, data->my_en.e_vdW );
//fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
fprintf( out_control->ecou, "%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,
r_ij, system->my_atoms[i].q, system->my_atoms[j].q,
e_ele, data->my_en.e_ele );
#endif
#ifdef TEST_FORCES
rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
#endif
}
}
}
Compute_Polarization_Energy( system, data );
}
void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists,
output_controls *out_control )
{
int i, j, pj, r, natoms;
int type_i, type_j, tmin, tmax;
int start_i, end_i, flag;
rc_tagint orig_i, orig_j;
double r_ij, base, dif;
double e_vdW, e_ele;
double CEvd, CEclmb, SMALL = 0.0001;
double f_tmp, delij[3];
rvec temp, ext_press;
far_neighbor_data *nbr_pj;
reax_list *far_nbrs;
LR_lookup_table *t;
natoms = system->n;
far_nbrs = (*lists) + FAR_NBRS;
e_ele = e_vdW = 0;
for( i = 0; i < natoms; ++i ) {
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
start_i = Start_Index(i,far_nbrs);
end_i = End_Index(i,far_nbrs);
orig_i = system->my_atoms[i].orig_id;
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
j = nbr_pj->nbr;
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
orig_j = system->my_atoms[j].orig_id;
flag = 0;
if(nbr_pj->d <= control->nonb_cut) {
if (j < natoms) flag = 1;
else if (orig_i < orig_j) flag = 1;
else if (orig_i == orig_j) {
if (nbr_pj->dvec[2] > SMALL) flag = 1;
else if (fabs(nbr_pj->dvec[2]) < SMALL) {
if (nbr_pj->dvec[1] > SMALL) flag = 1;
else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
flag = 1;
}
}
}
if (flag) {
r_ij = nbr_pj->d;
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 = (double)(r+1) * t->dx;
dif = r_ij - base;
e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
t->vdW[r].a;
e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
t->ele[r].a;
e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;
data->my_en.e_vdW += e_vdW;
data->my_en.e_ele += e_ele;
CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
t->CEvd[r].a;
CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
t->CEclmb[r].a;
CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;
/* tally into per-atom energy */
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
f_tmp = -(CEvd + CEclmb);
system->pair_ptr->ev_tally(i,j,natoms,1,e_vdW,e_ele,
f_tmp,delij[0],delij[1],delij[2]);
}
if( control->virial == 0 ) {
rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec );
}
else { // NPT, iNPT or sNPT
rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
rvec_ScaledAdd( workspace->f[i], -1., temp );
rvec_Add( workspace->f[j], temp );
rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
}
}
}
Compute_Polarization_Energy( system, data );
}
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 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 Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
storage *workspace, reax_list **lists )
{
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
rvec temp, ext_press;
ivec rel_box;
int pk, k, j;
/* Initializations */
nbr_j = &(bonds->select.bond_list[pj]);
j = nbr_j->nbr;
bo_ij = &(nbr_j->bo_data);
bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
rvec_Scale(temp, -coef.C2dbo, nbr_k->bo_data.dBOp); /*2nd, dBO*/
rvec_ScaledAdd(temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
rvec_ScaledAdd(temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); /*3rd, dBOpi*/
rvec_ScaledAdd(temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);/*3rd, dBOpi2*/
/* force */
rvec_Add( workspace->f[k], temp );
/* pressure */
rvec_iMultiply( ext_press, nbr_k->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
/* then atom i itself */
rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st,dBO*/
rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd,dBO*/
rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st,dBO*/
rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd,dBO*/
rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/
rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/
/* force */
rvec_Add( workspace->f[i], temp );
for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/
rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/
rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/
/* force */
rvec_Add( workspace->f[k], temp );
/* pressure */
if( k != i ) {
ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i)
rvec_iMultiply( ext_press, rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
}
/* then atom j itself */
rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/
rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/
rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/
rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/
rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/
rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/
/* force */
rvec_Add( workspace->f[j], temp );
/* pressure */
rvec_iMultiply( ext_press, nbr_j->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
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);
}
}
}
}
}
}
