void Reset_Neighbor_Lists( reax_system *system, control_params *control,
storage *workspace, reax_list **lists,
MPI_Comm comm )
{
int i, total_bonds, Hindex, total_hbonds;
reax_list *bonds, *hbonds;
/* bonds list */
if (system->N > 0) {
bonds = (*lists) + BONDS;
total_bonds = 0;
/* reset start-end indexes */
for( i = 0; i < system->N; ++i ) {
Set_Start_Index( i, total_bonds, bonds );
Set_End_Index( i, total_bonds, bonds );
total_bonds += system->my_atoms[i].num_bonds;
}
/* is reallocation needed? */
if (total_bonds >= bonds->num_intrs * DANGER_ZONE) {
workspace->realloc.bonds = 1;
if (total_bonds >= bonds->num_intrs) {
fprintf(stderr,
"p%d: not enough space for bonds! total=%d allocated=%d\n",
system->my_rank, total_bonds, bonds->num_intrs );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
if (control->hbond_cut > 0 && system->numH > 0) {
hbonds = (*lists) + HBONDS;
total_hbonds = 0;
/* reset start-end indexes */
for( i = 0; i < system->n; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if (Hindex > -1) {
Set_Start_Index( Hindex, total_hbonds, hbonds );
Set_End_Index( Hindex, total_hbonds, hbonds );
total_hbonds += system->my_atoms[i].num_hbonds;
}
}
/* is reallocation needed? */
if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) {
workspace->realloc.hbonds = 1;
if (total_hbonds >= hbonds->num_intrs) {
fprintf(stderr,
"p%d: not enough space for hbonds! total=%d allocated=%d\n",
system->my_rank, total_hbonds, hbonds->num_intrs );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
}
// copy bond list into old bond list
void Copy_Bond_List( reax_system *system, control_params *control,
list **lists )
{
int i, j, top_old;
list *new_bonds = (*lists) + BONDS;
list *old_bonds = (*lists) + OLD_BONDS;
for( top_old = 0, i = 0; i < system->N; ++i ) {
Set_Start_Index( i, top_old, old_bonds );
// fprintf( stdout, "%d: ", i );
for( j = Start_Index( i, new_bonds ); j < End_Index( i, new_bonds ); ++j )
if( new_bonds->select.bond_list[j].bo_data.BO >= control->bg_cut ) {
// fprintf( stderr, "%d ", new_bonds->select.bond_list[j].nbr );
old_bonds->select.bond_list[ top_old ].nbr =
new_bonds->select.bond_list[j].nbr;
old_bonds->select.bond_list[ top_old ].bo_data.BO =
new_bonds->select.bond_list[j].bo_data.BO;
top_old++;
}
Set_End_Index( i, top_old, old_bonds);
// fprintf( stderr, "--- s: %d, e: %d\n",
// Start_Index( i, old_bonds ), End_Index( i, old_bonds ) );
}
}
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 );
}
}
}
