void Validate_Lists( reax_system *system, storage *workspace, reax_list **lists,
int step, int n, int N, int numH, MPI_Comm comm )
{
int i, comp, Hindex;
reax_list *bonds, *hbonds;
reallocate_data *realloc;
realloc = &(workspace->realloc);
/* bond list */
if( N > 0 ) {
bonds = *lists + BONDS;
for( i = 0; i < N; ++i ) {
// if( i < n ) - we need to update ghost estimates for delayed nbrings
system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS);
//if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 )
//workspace->realloc.bonds = 1;
if( i < N-1 )
comp = Start_Index(i+1, bonds);
else comp = bonds->num_intrs;
if( End_Index(i, bonds) > comp ) {
fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, i, End_Index(i,bonds), comp );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
}
}
/* hbonds list */
if( numH > 0 ) {
hbonds = *lists + HBONDS;
for( i = 0; i < n; ++i ) {
Hindex = system->my_atoms[i].Hindex;
if( Hindex > -1 ) {
system->my_atoms[i].num_hbonds =
(int)(MAX( Num_Entries(Hindex, hbonds)*SAFER_ZONE, MIN_HBONDS ));
//if( Num_Entries(i, hbonds) >=
//(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){
// workspace->realloc.hbonds = 1;
if( Hindex < numH-1 )
comp = Start_Index(Hindex+1, hbonds);
else comp = hbonds->num_intrs;
if( End_Index(Hindex, hbonds) > comp ) {
fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n",
step, Hindex, End_Index(Hindex,hbonds), comp );
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 ) );
}
}
/* 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, static_storage *workspace, list **lists) {
int i, pj;
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->ensemble == NVE || control->ensemble == NVT)
Add_dBond_to_Forces(i, pj, system, data, workspace, lists);
else
Add_dBond_to_Forces_NPT(i, pj, system, data, workspace,
lists);
}
}
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 );
}
}
/* 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 Visit_Bonds( int atom, int *mark, int *type, reax_system *system,
control_params *control, list *bonds, int ignore )
{
int i, t, start, end, nbr;
real bo;
mark[atom] = 1;
t = system->atoms[atom].type;
if( ignore && control->ignore[t] )
return;
type[t]++;
start = Start_Index( atom, bonds );
end = End_Index( atom, bonds );
for( i = start; i < end; ++i ) {
nbr = bonds->select.bond_list[i].nbr;
bo = bonds->select.bond_list[i].bo_data.BO;
if( bo >= control->bg_cut && !mark[nbr] )
Visit_Bonds( nbr, mark, type, system, control, bonds, ignore );
}
}
void Get_Molecule( int atom, molecule *m, int *mark, reax_system *system,
control_params *control, list *bonds, int print,
FILE *fout )
{
int i, start, end;
start = Start_Index( atom, bonds );
end = End_Index( atom, bonds );
if( print )
fprintf( fout, "%5d(%2s)",
atom+1, system->reaxprm.sbp[ system->atoms[atom].type ].name );
mark[atom] = 1;
m->atom_list[ m->atom_count++ ] = atom;
m->mtypes[ system->atoms[ atom ].type ]++;
for( i = start; i < end; ++i )
if( bonds->select.bond_list[i].bo_data.BO >= control->bg_cut &&
!mark[bonds->select.bond_list[i].nbr] )
Get_Molecule( bonds->select.bond_list[i].nbr, m, mark,
system, control, bonds, print, fout );
}
void Estimate_Storage_Sizes(reax_system *system, control_params *control,
list **lists, int *Htop, int *hb_top, int *bond_top, int *num_3body) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
real r_ij, r2;
real C12, C34, C56;
real BO, BO_s, BO_pi, BO_pi2;
real p_boc1, p_boc2;
list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
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);
sbp_i = &(system->reaxprm.sbp[type_i]);
ihb = sbp_i->p_hbond;
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]);
type_j = atom_j->type;
sbp_j = &(system->reaxprm.sbp[type_j]);
twbp = &(system->reaxprm.tbp[type_i][type_j]);
if (nbr_pj->d <= control->r_cut) {
++(*Htop);
/* hydrogen bond lists */
if (control->hb_cut > 0.1 && (ihb == 1 || ihb == 2)
&& nbr_pj->d <= control->hb_cut) {
jhb = sbp_j->p_hbond;
if (ihb == 1 && jhb == 2)
++hb_top[i];
else if (ihb == 2 && jhb == 1)
++hb_top[j];
}
/* uncorrected bond orders */
if (nbr_pj->d <= control->nbr_cut) {
r_ij = nbr_pj->d;
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) {
++bond_top[i];
++bond_top[j];
}
}
}
}
}
*Htop += system->N;
*Htop *= SAFE_ZONE;
for (i = 0; i < system->N; ++i) {
hb_top[i] = MAX( hb_top[i] * SAFE_HBONDS, MIN_HBONDS );
*num_3body += SQR(bond_top[i]);
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
}
*num_3body *= SAFE_ZONE;
}
void Validate_Lists(static_storage *workspace, list **lists, int step, int n,
int Hmax, int Htop, int num_bonds, int num_hbonds) {
int i, flag;
list *bonds, *hbonds;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
/* far neighbors */
if (Htop > Hmax * DANGER_ZONE) {
workspace->realloc.Htop = Htop;
if (Htop > Hmax) {
fprintf(stderr,
"step%d - ran out of space on H matrix: Htop=%d, max = %d",
step, Htop, Hmax);
exit(INSUFFICIENT_SPACE);
}
}
/* bond list */
flag = -1;
workspace->realloc.num_bonds = num_bonds;
for (i = 0; i < n - 1; ++i)
if (End_Index(i, bonds) >= Start_Index(i + 1, bonds) - 2) {
workspace->realloc.bonds = 1;
if (End_Index(i, bonds) > Start_Index(i + 1, bonds))
flag = i;
}
if (flag > -1) {
fprintf(stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, bonds),
Start_Index(flag + 1, bonds));
exit(INSUFFICIENT_SPACE);
}
if (End_Index(i, bonds) >= bonds->num_intrs - 2) {
workspace->realloc.bonds = 1;
if (End_Index(i, bonds) > bonds->num_intrs) {
fprintf(stderr,
"step%d-bondchk failed: i=%d end(i)=%d bond_end=%d\n",
step, flag, End_Index(i, bonds), bonds->num_intrs);
exit(INSUFFICIENT_SPACE);
}
}
/* hbonds list */
if (workspace->num_H > 0) {
flag = -1;
workspace->realloc.num_hbonds = num_hbonds;
for (i = 0; i < workspace->num_H - 1; ++i)
if (Num_Entries(i, hbonds) >= (Start_Index(i + 1, hbonds)
- Start_Index(i, hbonds)) * DANGER_ZONE) {
workspace->realloc.hbonds = 1;
if (End_Index(i, hbonds) > Start_Index(i + 1, hbonds))
flag = i;
}
if (flag > -1) {
fprintf(stderr,
"step%d-hbondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
step, flag, End_Index(flag, hbonds), Start_Index(flag + 1,
hbonds));
exit(INSUFFICIENT_SPACE);
}
if (Num_Entries(i, hbonds) >= (hbonds->num_intrs - Start_Index(i,
hbonds)) * DANGER_ZONE) {
workspace->realloc.hbonds = 1;
if (End_Index(i, hbonds) > hbonds->num_intrs) {
fprintf(stderr,
"step%d-hbondchk failed: i=%d end(i)=%d hbondend=%d\n",
step, flag, End_Index(i, hbonds), hbonds->num_intrs);
exit(INSUFFICIENT_SPACE);
}
}
}
}
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 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 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 BO( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, reax_list **lists, output_controls *out_control )
{
int i, j, pj, type_i, type_j;
int start_i, end_i, sym_index;
double val_i, Deltap_i, Deltap_boc_i;
double val_j, Deltap_j, Deltap_boc_j;
double f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
double exp_p1i, exp_p2i, exp_p1j, exp_p2j;
double temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji;
double Cf45_ij, Cf45_ji, p_lp1; //u_ij, u_ji
double A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji;
double explp1, p_boc1, p_boc2;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_order_data *bo_ij, *bo_ji;
reax_list *bonds = (*lists) + BONDS;
p_boc1 = system->reax_param.gp.l[0];
p_boc2 = system->reax_param.gp.l[1];
/* Calculate Deltaprime, Deltaprime_boc values */
for( i = 0; i < system->N; ++i ) {
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
workspace->Deltap_boc[i] =
workspace->total_bond_order[i] - sbp_i->valency_val;
workspace->total_bond_order[i] = 0;
}
/* Corrected Bond Order calculations */
for( i = 0; i < system->N; ++i ) {
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
val_i = sbp_i->valency;
Deltap_i = workspace->Deltap[i];
Deltap_boc_i = workspace->Deltap_boc[i];
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
bo_ij = &( bonds->select.bond_list[pj].bo_data );
// fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
if( i < j || workspace->bond_mark[j] > 3 ) {
twbp = &( system->reax_param.tbp[type_i][type_j] );
if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
bo_ij->C1dbo = 1.000000;
bo_ij->C2dbo = 0.000000;
bo_ij->C3dbo = 0.000000;
bo_ij->C1dbopi = bo_ij->BO_pi;
bo_ij->C2dbopi = 0.000000;
bo_ij->C3dbopi = 0.000000;
bo_ij->C4dbopi = 0.000000;
bo_ij->C1dbopi2 = bo_ij->BO_pi2;
bo_ij->C2dbopi2 = 0.000000;
bo_ij->C3dbopi2 = 0.000000;
bo_ij->C4dbopi2 = 0.000000;
}
else {
val_j = system->reax_param.sbp[type_j].valency;
Deltap_j = workspace->Deltap[j];
Deltap_boc_j = workspace->Deltap_boc[j];
/* on page 1 */
if( twbp->ovc >= 0.001 ) {
/* Correction for overcoordination */
exp_p1i = exp( -p_boc1 * Deltap_i );
exp_p2i = exp( -p_boc2 * Deltap_i );
exp_p1j = exp( -p_boc1 * Deltap_j );
exp_p2j = exp( -p_boc2 * Deltap_j );
f2 = exp_p1i + exp_p1j;
f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
( val_j + f2 )/( val_j + f2 + f3 ) );
temp = f2 + f3;
u1_ij = val_i + temp;
u1_ji = val_j + temp;
Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) +
1.0 / SQR( u1_ji ));
Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
( u1_ji - f3 ) / SQR( u1_ji ));
Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
((val_i+f2) / SQR(u1_ij)) *
( -p_boc1 * exp_p1i +
exp_p2i / ( exp_p2i + exp_p2j ) ) +
-p_boc1 * exp_p1i / u1_ji -
((val_j+f2) / SQR(u1_ji)) *
( -p_boc1 * exp_p1i +
exp_p2i / ( exp_p2i + exp_p2j ) ));
Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
}
else {
/* No overcoordination correction! */
f1 = 1.0;
Cf1_ij = Cf1_ji = 0.0;
}
if( twbp->v13cor >= 0.001 ) {
/* Correction for 1-3 bond orders */
exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
exp_f5 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
f4 = 1. / (1. + exp_f4);
f5 = 1. / (1. + exp_f5);
f4f5 = f4 * f5;
/* Bond Order pages 8-9, derivative of f4 and f5 */
Cf45_ij = -f4 * exp_f4;
Cf45_ji = -f5 * exp_f5;
}
else {
f4 = f5 = f4f5 = 1.0;
Cf45_ij = Cf45_ji = 0.0;
}
/* Bond Order page 10, derivative of total bond order */
A0_ij = f1 * f4f5;
A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
(Cf45_ij + Cf45_ji);
A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
A3_ij = A2_ij + Cf1_ij / f1;
A3_ji = A2_ji + Cf1_ji / f1;
/* find corrected bond orders and their derivative coef */
bo_ij->BO = bo_ij->BO * A0_ij;
bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
bo_ij->C2dbo = bo_ij->BO * A2_ij;
bo_ij->C3dbo = bo_ij->BO * A2_ji;
bo_ij->C1dbopi = f1*f1*f4*f5;
bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
bo_ij->C1dbopi2 = f1*f1*f4*f5;
bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
}
/* neglect bonds that are < 1e-10 */
if( bo_ij->BO < 1e-10 )
bo_ij->BO = 0.0;
if( bo_ij->BO_s < 1e-10 )
bo_ij->BO_s = 0.0;
if( bo_ij->BO_pi < 1e-10 )
bo_ij->BO_pi = 0.0;
if( bo_ij->BO_pi2 < 1e-10 )
bo_ij->BO_pi2 = 0.0;
workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO
}
else {
/* We only need to update bond orders from bo_ji
everything else is set in uncorrected_bo calculations */
sym_index = bonds->select.bond_list[pj].sym_index;
bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
bo_ij->BO = bo_ji->BO;
bo_ij->BO_s = bo_ji->BO_s;
bo_ij->BO_pi = bo_ji->BO_pi;
bo_ij->BO_pi2 = bo_ji->BO_pi2;
workspace->total_bond_order[i] += bo_ij->BO;// now keeps total_BO
}
}
}
p_lp1 = system->reax_param.gp.l[15];
for( j = 0; j < system->N; ++j ){
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[ type_j ]);
workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e;
workspace->Delta_boc[j] = workspace->total_bond_order[j] -
sbp_j->valency_boc;
workspace->Delta_val[j] = workspace->total_bond_order[j] -
sbp_j->valency_val;
workspace->vlpex[j] = workspace->Delta_e[j] -
2.0 * (int)(workspace->Delta_e[j]/2.0);
explp1 = exp(-p_lp1 * SQR(2.0 + workspace->vlpex[j]));
workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]);
workspace->dDelta_lp[j] = workspace->Clp[j];
if( sbp_j->mass > 21.0 ) {
workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
workspace->dDelta_lp_temp[j] = 0.;
}
else {
workspace->nlp_temp[j] = workspace->nlp[j];
workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
workspace->dDelta_lp_temp[j] = workspace->Clp[j];
}
}
}
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 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 Report_Bond_Change( reax_system *system, control_params *control,
static_storage *workspace, list *old_bonds,
list *new_bonds, int a1, int a2, int flag,
FILE *fout )
{
int i;
int rev1, rev2;
int mol1 = -1, mol2 = -1;
// which molecule the atom belongs to, 0: Silica, 1: Water
rev1 = workspace->orig_id[a1];
rev2 = workspace->orig_id[a2];
if( !strcmp( system->atoms[a1].name, " Si" ) ||
!strcmp( system->atoms[a1].name, " O" ) )
mol1 = 0;
else mol1 = 1;
if( !strcmp( system->atoms[a2].name, " Si" ) ||
!strcmp( system->atoms[a2].name, " O" ) )
mol2 = 0;
else mol2 = 1;
if( mol1 == 0 && mol2 == 0 ) { // silica-silica
if( flag )
fprintf( fout, "silica bond formation:" );
else fprintf( fout, "silica bond breakage :" );
fprintf( fout, "%5d(%s)-%5d(%s)\n",
rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
}
else if( mol1 == 1 && mol2 == 1 ) { // water-water
if( flag )
fprintf( fout, "water bond formation:" );
else fprintf( fout, "water bond breakage :" );
fprintf( fout, "%5d(%s)-%5d(%s)\n",
rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
}
else { // water-silica!
if( flag )
fprintf( fout, "SILICA-WATER bond formation:" );
else fprintf( fout, "SILICA-WATER bond breakage :" );
fprintf( fout, "%5d(%s)-%5d(%s)\n",
rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
fprintf( fout, "%5d(%s) was connected to:", rev1, system->atoms[a1].name );
for( i = Start_Index(a1, old_bonds); i < End_Index(a1, old_bonds); ++i )
if( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
fprintf( fout, " %5d(%s)",
workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
fprintf( fout, "\n" );
fprintf( fout, "%5d(%s) was connected to:", rev2, system->atoms[a2].name );
for( i = Start_Index(a2, old_bonds); i < End_Index(a2, old_bonds); ++i )
if( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
fprintf( fout, " %5d(%s)",
workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
fprintf( fout, "\n" );
}
}
void Compute_Bond_Boost_Force(reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace, list **lists,
output_controls *out_control) {
int i, j, pj;
int type_i, type_j;
int adatom, adatom2; // label the boost atom
int nbond, nrad; // Nb
int start_i, end_i;
real e, emax, r, re, r_max; // eta, eta_max, r, r_e
real bo;
real A, dA, V; // A(\eta^max), and \Delta A(\eta^max)
real *rv, *rv_max;
real q, P1, vmax; // q, P1 in equation 13
real S1, S2, f1, f2, C1, C2;
real bf; // boost force scale
rvec df; // boost force
reax_atom *atom1, *atom2;
bond_order_data *bo_ij;
two_body_parameters *twbp;
list *bonds;
nrad = Find_Radicals(system, control, data, workspace, lists, out_control);
//printf("-------------------------step %d -----------------\n", data->step);
bonds = (*lists) + BONDS;
// bond boost parameters
q = control->bboost_q; // should read this from control file
P1 = control->bboost_P1;
vmax = control->bboost_Vmax;
// initiate parameters
e = 0;
adatom = 0;
adatom2 = 0;
nbond = 0;
emax = 0.0;
bo = 0.0;
re = 0.001;
A = 0.0;
dA = 0.0;
r_max = 0.0;
// first get the max bond order
for( i=0; i < system->N; ++i ) {
re = 0.001;
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ){
if( i < bonds->select.bond_list[pj].nbr ) {
j = bonds->select.bond_list[pj].nbr;
type_i = system->atoms[i].type;
type_j = system->atoms[j].type;
twbp = &( system->reaxprm.tbp[type_i][type_j] );
bo_ij = &( bonds->select.bond_list[pj].bo_data );
re = twbp->r_e; // get r_e from ffield.ext
r = bonds->select.bond_list[pj].d;
e = (r - re)/re; // eta
//printf("r = %f, re = %f, e = %f\n", r, re, e);
bo = bo_ij->BO;
if ( (fabs (emax) < fabs(e)) & (bo > q)) {
emax = e;
adatom = i;
adatom2 = j;
}
}
}
}
/*
printf("atom1 = %s ", system->reaxprm.sbp[ system->atoms[adatom].type ].name);
printf("atom2 = %s ", system->reaxprm.sbp[ system->atoms[adatom2].type ].name);
printf("bo = %f\n", bo);
*/
V = 0.0; // boost energy
if (fabs(emax) < q && nrad == 0) {
i = adatom;
vmax = control->bboost_Vmax;
// calculate A, and dA
S1 = emax/q;
S2 = S1 * S1;
C1 = 1 - (emax/q)*(emax/q);
C2 = 1 - P1*P1*S2;
A = C1 * C1 / C2;
/*
printf("S1 = %f, S2 = %f ", S1, S2);
printf("C1 = %f, C2 = %f ", C1, C2);
printf("A = %f, emax = %f\n", A, emax);
*/
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ) {
if( i < bonds->select.bond_list[pj].nbr ) {
bo_ij = &( bonds->select.bond_list[pj].bo_data );
bo = bo_ij->BO;
if (bo > 0.3)
nbond += 1;
}
}
for( pj = start_i; pj < end_i; ++pj ) {
if( i < bonds->select.bond_list[pj].nbr ) {
bo_ij = &( bonds->select.bond_list[pj].bo_data );
bo = bo_ij->BO;
if (bo > 0.3) {
j = bonds->select.bond_list[pj].nbr;
r = bonds->select.bond_list[pj].d;
rv = bonds->select.bond_list[pj].dvec;
type_i = system->atoms[i].type;
type_j = system->atoms[j].type;
twbp = &( system->reaxprm.tbp[type_i][type_j] );
vmax = twbp->v_max;
re = twbp->r_e; // get r_e from ffield.ext
e = (r - re)/re; // eta
C1 = 1 - e*e/(q*q);
V += vmax / nbond * C1;
bf = 2*A*vmax*e/(nbond*q*re);
/*
printf("e = %.3f, emax = %.3f, C1 = %.3f, re = %.3f, V = %.3f, A = %.3f bf = %.3f, vmax = %.3f, \n",\
e, emax, C1, re, V, A, bf, vmax);
*/
if (fabs(e - emax) < 0.00001) {
C2 = 1 - e*e*P1*P1/(q*q);
f1 = 2/(q*re);
f2 = f1/2*P1*P1;
dA = 2*e*C1/C2*(f1 - f2*C1/C2);
rv_max = bonds->select.bond_list[pj].dvec;
r_max = bonds->select.bond_list[pj].d;;
}
rvec_Scale(df, bf, rv);
//rvec_Scale(df, 1/r, df);
// assign the boost force
atom1 = &( system->atoms[i] );
atom2 = &( system->atoms[j] );
/* printf("ofx = %8.3f ofy = %8.3f ofz = %8.3f \n", system->atoms[i].f[0],\
system->atoms[i].f[1], system->atoms[i].f[2]);
*/
rvec_Add(system->atoms[i].f, df);
//printf(" fx = %8.3f fy = %8.3f fz = %8.3f \n", df[0], df[1], df[2]);
/*
rvec_Scale(df, -1, df);
rvec_Add(system->atoms[j].f, df);
*/
}
}
}
// add the contribution of evalope function A
bf = dA * V;
rvec_Scale(df, bf, rv_max);
//rvec_Scale(df, 1/r_max, df);
//printf("Max bf = %8.3f\n", bf);
/*
printf("Mfx = %8.3f Mfy = %8.3f Mfz = %8.3f dA = %8.3f V = %8.3f emax = %8.3f \n",\
df[0], df[1], df[2], dA, V, emax);
*/
atom1 = &( system->atoms[i] );
rvec_Add(system->atoms[i].f, df);
}
fprintf( out_control->bboost, "%-10d%6d%6d%10.4f%10.4f%10.4f", \
data->step, adatom + 1, adatom2 + 1, bo, emax, A*V );
fprintf( out_control->bboost, " %4s %4s\n", \
system->reaxprm.sbp[ system->atoms[adatom].type ].name,
system->reaxprm.sbp[ system->atoms[adatom2].type ].name);
fflush( out_control->bboost);
}
// ASSUMPTION: Bond lists are sorted
int Compare_Bond_Lists( int atom, control_params *control, list **lists )
{
int oldp, newp;
list *new_bonds = (*lists) + BONDS;
list *old_bonds = (*lists) + OLD_BONDS;
/*fprintf( stdout, "\n%d\nold_bonds:", atom );
for( oldp = Start_Index( atom, old_bonds );
oldp < End_Index( atom, old_bonds ); ++oldp )
if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
fprintf( stdout, "%5d", old_bonds->select.bond_list[oldp].nbr );
fprintf( stdout, "\nnew_bonds:" );
for( newp = Start_Index( atom, new_bonds );
newp < End_Index( atom, new_bonds ); ++newp )
if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
fprintf( stdout, "%5d", new_bonds->select.bond_list[newp].nbr );*/
for( oldp = Start_Index( atom, old_bonds ),
newp = Start_Index( atom, new_bonds );
oldp < End_Index(atom, old_bonds) || newp < End_Index(atom, new_bonds);
oldp = MIN( oldp + 1, End_Index( atom, old_bonds ) ),
newp = MIN( newp + 1, End_Index( atom, new_bonds ) ) ) {
while( oldp < End_Index( atom, old_bonds ) &&
old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
++oldp;
while( newp < End_Index( atom, new_bonds ) &&
new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
++newp;
/*fprintf( fout, "%d, oldp: %d - %d, newp: %d - %d",
atom, oldp, old_bonds->select.bond_list[oldp].nbr,
newp, new_bonds->select.bond_list[newp].nbr );*/
if( oldp < End_Index( atom, old_bonds ) ) {
/* there are some other bonds in the old list */
if( newp < End_Index( atom, new_bonds ) ) {
if( old_bonds->select.bond_list[oldp].nbr !=
new_bonds->select.bond_list[newp].nbr ) {
//fprintf( fout, " --> case1, return 1\n" );
return 1;
}
}
else {
/* there is no other bond in the new list */
//fprintf( fout, " --> case2, return 1\n" );
return 1;
}
}
else {
/* there are no more bonds in old_bond list */
if( newp < End_Index( atom, new_bonds ) ) {
/* there is at least one other bond in the new list */
//fprintf( fout, " --> case 3, return 1\n" );
return 1;
}
else {
/* there is no other bond in the new list, either */
//fprintf( fout, " --> case 4, return 0\n" );
return 0;
}
}
}
return 0;
}
void Analyze_Silica( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list **lists, FILE *fout )
{
int atom, i, j, k, pi, pk, pk_j, newp, coord;
int O_SI_O_count, SI_O_SI_count;
int si_coord[10], ox_coord[10];
real O_SI_O, SI_O_SI;
list *new_bonds = (*lists) + BONDS;
list *thb_intrs = (*lists) + THREE_BODIES;
Analyze_Fragments( system, control, data, workspace, lists, fout, 0 );
/* analyze atom coordinations */
for( i = 0; i < 10; ++i )
si_coord[i] = ox_coord[i] = 0;
for( atom = 0; atom < system->N; ++atom ) {
coord = 0;
for( newp = Start_Index( atom, new_bonds );
newp < End_Index( atom, new_bonds ); ++newp )
if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
++coord;
if( system->atoms[ atom ].type == SI_ATOM ) {
/*if( coord == 4 )
full_coord_SI++;
else less_coord_SI++;*/
++si_coord[coord];
}
else if( system->atoms[ atom ].type == O_ATOM ) {
/*if( coord == 2 )
full_coord_O++;
else less_coord_O++;*/
++ox_coord[coord];
}
}
/* fprintf( fout, "\nFour Coordinated SI: %.2f%\n",
(double)full_coord_SI / (full_coord_SI + less_coord_SI) * 100. );
fprintf( fout, "Four Coordinated O : %.2f%\n",
(double)full_coord_O / (full_coord_O + less_coord_O ) * 100. ); */
fprintf( fout, "Silicon coordinations:\n" );
for( i = 1; i < 10; ++i )
if( si_coord[i] )
fprintf( fout, "\t%d-coord: %d\n", i, si_coord[i] );
fprintf( fout, "\nOxygen coordinations:\n" );
for( i = 1; i < 10; ++i )
if( ox_coord[i] )
fprintf( fout, "\t%d-coord: %d\n", i, ox_coord[i] );
/* analyze bond angles */
O_SI_O = 0;
O_SI_O_count = 0;
SI_O_SI = 0;
SI_O_SI_count = 0;
for( j = 0; j < system->N; ++j )
if( system->atoms[j].type == O_ATOM || system->atoms[j].type == SI_ATOM )
for( pi = Start_Index(j, new_bonds); pi < End_Index(j, new_bonds); ++pi )
if( new_bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut ) {
i = new_bonds->select.bond_list[pi].nbr;
if(system->atoms[i].type==O_ATOM || system->atoms[i].type==SI_ATOM) {
for( pk = Start_Index( pi, thb_intrs );
pk < End_Index( pi, thb_intrs ); ++pk ) {
k = thb_intrs->select.three_body_list[pk].thb;
pk_j = thb_intrs->select.three_body_list[pk].pthb;
// get k's pointer on j's bond list
if( new_bonds->select.bond_list[pk_j].bo_data.BO >=
control->bg_cut ) { // physical j&k bond
/*fprintf( fout, "%5d(%d) %5d(%d) %5d(%d) %8.3f\n",
i, system->atoms[i].type, j, system->atoms[j].type,
k, system->atoms[k].type,
thb_intrs->select.three_body_list[pk].theta );*/
if( system->atoms[i].type == O_ATOM &&
system->atoms[j].type == SI_ATOM &&
system->atoms[k].type == O_ATOM ){
O_SI_O_count++;
O_SI_O += thb_intrs->select.three_body_list[pk].theta;
}
else if ( system->atoms[i].type == SI_ATOM &&
system->atoms[j].type == O_ATOM &&
system->atoms[k].type == SI_ATOM ){
SI_O_SI_count++;
SI_O_SI += thb_intrs->select.three_body_list[pk].theta;
}
}
}
}
}
fprintf( fout, "\nAverage O-Si-O angle: %8.2f\n",
RAD2DEG(O_SI_O / O_SI_O_count) );
fprintf( fout, "Average Si-O-Si angle: %8.2f\n\n\n",
RAD2DEG(SI_O_SI / SI_O_SI_count) );
fflush( fout );
}
/* ASSUMPTION: Bond lists are sorted */
void Compare_Bonding( int atom, reax_system *system, control_params *control,
static_storage *workspace, list *old_bonds,
list *new_bonds, FILE *fout )
{
int oldp, newp;
/* fprintf( fout, "\n%d\nold_bonds:", atom );
for( oldp = Start_Index( atom, old_bonds );
oldp < End_Index( atom, old_bonds ); ++oldp )
if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
fprintf( fout, "%5d", old_bonds->select.bond_list[oldp].nbr );
fprintf( fout, "\nnew_bonds:" );
for( newp = Start_Index( atom, new_bonds );
newp < End_Index( atom, new_bonds ); ++newp )
if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
fprintf( fout, "%6d", new_bonds->select.bond_list[newp].nbr );
fprintf( fout, "\n" ); */
for( oldp = Start_Index( atom, old_bonds );
oldp < End_Index( atom, old_bonds ) &&
old_bonds->select.bond_list[oldp].nbr < atom;
++oldp );
for( newp = Start_Index( atom, new_bonds );
newp < End_Index( atom, new_bonds ) &&
new_bonds->select.bond_list[newp].nbr < atom;
++newp );
while( oldp < End_Index( atom, old_bonds ) ||
newp < End_Index( atom, new_bonds ) ) {
while( oldp < End_Index( atom, old_bonds ) &&
old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
++oldp;
while( newp < End_Index( atom, new_bonds ) &&
new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
++newp;
/*fprintf( fout, "%d, oldp: %d - %d: %f newp: %d - %d: %f",
atom, oldp, old_bonds->select.bond_list[oldp].nbr,
old_bonds->select.bond_list[oldp].bo_data.BO,
newp, new_bonds->select.bond_list[newp].nbr,
new_bonds->select.bond_list[newp].bo_data.BO ); */
if( oldp < End_Index( atom, old_bonds ) ) {
/* there are some more bonds in the old list */
if( newp < End_Index( atom, new_bonds ) ) {
if( old_bonds->select.bond_list[oldp].nbr <
new_bonds->select.bond_list[newp].nbr ) {
// fprintf( fout, "%5d-%5d bond broken\n",
// atom, old_bonds->select.bond_list[oldp].nbr );
Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
atom, old_bonds->select.bond_list[oldp].nbr, 0,
fout );
++oldp;
}
else if( old_bonds->select.bond_list[oldp].nbr >
new_bonds->select.bond_list[newp].nbr ) {
// fprintf( fout, "%5d-%5d bond formed\n",
// atom, new_bonds->select.bond_list[newp].nbr );
Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
atom, new_bonds->select.bond_list[newp].nbr, 1,
fout );
++newp;
}
else
++newp, ++oldp;
}
else
/* there is no other bond in the new list */
while( oldp < End_Index( atom, old_bonds ) ) {
if( old_bonds->select.bond_list[oldp].bo_data.BO>=control->bg_cut ) {
// fprintf( fout, "%5d-%5d bond broken\n",
// atom, old_bonds->select.bond_list[oldp].nbr );
Report_Bond_Change( system, control, workspace,
old_bonds, new_bonds, atom,
old_bonds->select.bond_list[oldp].nbr, 0,
fout );
}
++oldp;
}
}
else {
/* there are no more bonds in old_bond list */
if( newp < End_Index( atom, new_bonds ) )
/* there is at least one other bond in the new list */
while( newp < End_Index( atom, new_bonds ) ) {
if( new_bonds->select.bond_list[newp].bo_data.BO>=control->bg_cut ){
// fprintf( fout, "%5d-%5d bond formed\n",
// atom, new_bonds->select.bond_list[newp].nbr );
Report_Bond_Change( system, control, workspace,
old_bonds, new_bonds, atom,
new_bonds->select.bond_list[newp].nbr, 1,
fout );
}
++newp;
}
else {
/* there is no other bond in the new list, either --
no need to do anything */
}
}
}
}
void Compute_Bond_Boost_Force_All_Couple(reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace, list **lists,
output_controls *out_control) {
int i, j, pj;
int type_i, type_j;
int adatom, adatom2; // label the boost atom
int nbond, nrad; // Nb
int start_i, end_i;
real e, emax, r, re, r_max; // eta, eta_max, r, r_e
real bo;
real A, dA, V; // A(\eta^max), and \Delta A(\eta^max)
real *rv, *rv_max;
real q, P1, vmax; // q, P1 in equation 13
real S1, S2, f1, f2, C1, C2;
real T;
real bf, bfactor; // boost force scale
rvec df; // boost force
reax_atom *atom1, *atom2;
bond_order_data *bo_ij;
two_body_parameters *twbp;
list *bonds;
nrad = Find_Radicals(system, control, data, workspace, lists, out_control);
//nrad = 0;
//printf("-------------------------step %d -----------------\n", data->step);
bonds = (*lists) + BONDS;
// bond boost parameters
q = control->bboost_q; // should read this from control file
P1 = control->bboost_P1;
vmax = control->bboost_Vmax;
// initiate parameters
e = 0;
adatom = 0;
adatom2 = 0;
bo = 0.0;
re = 0.001;
A = 0.0;
dA = 0.0;
r_max = 0.0;
bfactor = 1.0;
T = control->T_final;
V = 0.0; // bost energy
nbond = 0;
emax = 0.0;
// first get the max bond order
for( i=0; i < system->N; ++i ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ){
if( i < bonds->select.bond_list[pj].nbr ) {
j = bonds->select.bond_list[pj].nbr;
type_i = system->atoms[i].type;
type_j = system->atoms[j].type;
twbp = &( system->reaxprm.tbp[type_i][type_j] );
vmax = control->bboost_Vmax;
vmax = twbp->v_max;
bo_ij = &( bonds->select.bond_list[pj].bo_data );
re = twbp->r_e; // get r_e from ffield.ext
r = bonds->select.bond_list[pj].d;
e = (r - re)/re; // eta
bo = bo_ij->BO;
if (bo > q && vmax > 0) {
nbond += 1;
if ( fabs(emax) < fabs(e) ) {
emax = e;
adatom = i;
adatom2 = j;
/* for debug
printf("i = %d, j = %d, re = %.2f, r = %.2f ", i, j, re, r);
printf("x1 = %.2f, y1 = %.2f, z1 = %.2f, ", \
system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2]);
printf("x2 = %.2f, y2 = %.2f, z2 = %.2f\n", \
system->atoms[j].x[0], system->atoms[j].x[1], system->atoms[j].x[2]);
printf( " %4s %4s\n", \
system->reaxprm.sbp[ system->atoms[i].type ].name,
system->reaxprm.sbp[ system->atoms[j].type ].name);
*/
rv_max = bonds->select.bond_list[pj].dvec;
r_max = bonds->select.bond_list[pj].d;;
}
}
}
}
}
int ntmp;
if (fabs(emax) < q && nbond > 0 && nrad <= control->bboost_nrad) {
data->boost ++ ;
// calculate A, and dA
S1 = emax/q;
S2 = S1 * S1;
C1 = 1 - (emax/q)*(emax/q);
C2 = 1 - P1*P1*S2;
A = C1 * C1 / C2;
ntmp = 0;
for( i=0; i < system->N; ++i ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ) {
if( i < bonds->select.bond_list[pj].nbr ) {
j = bonds->select.bond_list[pj].nbr;
type_i = system->atoms[i].type;
type_j = system->atoms[j].type;
twbp = &( system->reaxprm.tbp[type_i][type_j] );
vmax = control->bboost_Vmax;
vmax = twbp->v_max;
bo_ij = &( bonds->select.bond_list[pj].bo_data );
r = bonds->select.bond_list[pj].d;
re = twbp->r_e; // get r_e from ffield.ext
rv = bonds->select.bond_list[pj].dvec;
bo = bo_ij->BO;
if (bo > q && vmax > 0) {
e = (r - re)/re; // eta
C1 = 1 - e*e/(q*q);
V += vmax / nbond * C1;
bf = 2*A*vmax*e/(nbond*q*q*re);
if (fabs(e - emax) < 0.00001) {
C2 = 1 - e*e*P1*P1/(q*q);
f1 = 2/(q*q*re);
f2 = f1/2*P1*P1;
dA = 2*e*C1/C2*(f1 - f2*C1/C2);
}
rvec_Scale(df, bf, rv);
atom1 = &( system->atoms[i] );
atom2 = &( system->atoms[j] );
rvec_Add(system->atoms[i].f, df);
rvec_ScaledAdd(system->atoms[j].f, -1, df);
ntmp++;
}
}
}
}
// add the contribution of evalope function A
bf = dA * V;
rvec_Scale(df, bf, rv_max);
atom1 = &( system->atoms[adatom]);
rvec_Add(system->atoms[adatom].f, df);
rvec_ScaledAdd(system->atoms[adatom2].f, -1, df);
}
else {
data->boost = 0;
}
bfactor = exp(4184 * A * V/(T * 8.314));
//bfactor = V;
fprintf( out_control->bboost, "%-10d%6d%6d%6d%3d%8.4f%8.4f %44.4f", \
data->step, nbond, adatom, adatom2, nrad, r_max, emax, bfactor );
fprintf( out_control->bboost, " %4s %4s\n", \
system->reaxprm.sbp[ system->atoms[adatom].type ].name,
system->reaxprm.sbp[ system->atoms[adatom2].type ].name);
fflush( out_control->bboost);
}
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control, MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int Htop, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
real r_ij, cutoff;
sparse_matrix *H;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for( i = system->n; i < system->N; ++i ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
//workspace->done_after[i] = Start_Index( i, far_nbrs );
}
H = workspace->H;
H->n = system->n;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local ) {
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
if( control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
//fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
// j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
if( renbr ) {
if(nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ){
type_j = atom_j->type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* H matrix entry */
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
H->entries[Htop].j = j;
//fprintf( stdout, "%d%d %d %d\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id) );
if( control->tabulate == 0 )
H->entries[Htop].val = Compute_H(r_ij,twbp->gamma,workspace->Tap);
else H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
++Htop;
}
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//if( workspace->bond_mark[i] == 1000 )
// workspace->done_after[i] = pj;
}
//fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local ) {
H->end[i] = Htop;
if( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
//fprintf( stderr, "after the first init loop\n" );
/*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
Set_End_Index(i, start_i, bonds );
}*/
/*for( i = system->n; i < system->N; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = workspace->done_after[i];
if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
}
}*/
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
system->my_rank, data->step, Htop, num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
#if defined( DEBUG )
Print_Bonds( system, bonds, "debugbonds.out" );
Print_Bond_List2( system, bonds, "pbonds.out" );
Print_Sparse_Matrix( system, H );
for( i = 0; i < H->n; ++i )
for( j = H->start[i]; j < H->end[i]; ++j )
fprintf( stderr, "%d %d %.15e\n",
MIN(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
MAX(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
H->entries[j].val );
#endif
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
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 Atom_Energy( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control )
{
int i, j, pj, type_i, type_j;
real Delta_lpcorr, dfvl;
real e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi;
real e_lph, Di, vov3, deahu2dbo, deahu2dsbo;
real e_ov, CEover1, CEover2, CEover3, CEover4;
real exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2;
real exp_ovun2n, exp_ovun6, exp_ovun8;
real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
real e_un, CEunder1, CEunder2, CEunder3, CEunder4;
real p_lp2, p_lp3;
real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
real eng_tmp;
int numbonds;
single_body_parameters *sbp_i;
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
reax_list *bonds = (*lists) + BONDS;
/* Initialize parameters */
p_lp3 = system->reax_param.gp.l[5];
p_ovun3 = system->reax_param.gp.l[32];
p_ovun4 = system->reax_param.gp.l[31];
p_ovun6 = system->reax_param.gp.l[6];
p_ovun7 = system->reax_param.gp.l[8];
p_ovun8 = system->reax_param.gp.l[9];
for( i = 0; i < system->n; ++i ) {
/* set the parameter pointer */
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[ type_i ]);
/* lone-pair Energy */
p_lp2 = sbp_i->p_lp2;
expvd2 = exp( -75 * workspace->Delta_lp[i] );
inv_expvd2 = 1. / (1. + expvd2 );
numbonds = 0;
e_lp = 0.0;
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
numbonds ++;
/* calculate the energy */
if (numbonds > 0)
data->my_en.e_lp += e_lp =
p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
dElp = p_lp2 * inv_expvd2 +
75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
CElp = dElp * workspace->dDelta_lp[i];
if (numbonds > 0) workspace->CdDelta[i] += CElp; // lp - 1st term
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0);
/* correction for C2 */
if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") )
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) {
twbp = &( system->reax_param.tbp[type_i][type_j]);
bo_ij = &( bonds->select.bond_list[pj].bo_data );
Di = workspace->Delta[i];
vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.);
if( vov3 > 3. ) {
data->my_en.e_lp += e_lph = p_lp3 * SQR(vov3-3.0);
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*pow(Di, 3.));
bo_ij->Cdbo += deahu2dbo;
workspace->CdDelta[i] += deahu2dsbo;
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0);
}
}
}
}
for( i = 0; i < system->n; ++i ) {
type_i = system->my_atoms[i].type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[ type_i ]);
/* over-coordination energy */
if( sbp_i->mass > 21.0 )
dfvl = 0.0;
else dfvl = 1.0; // only for 1st-row elements
p_ovun2 = sbp_i->p_ovun2;
sum_ovun1 = sum_ovun2 = 0;
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
bo_ij = &(bonds->select.bond_list[pj].bo_data);
twbp = &(system->reax_param.tbp[ type_i ][ type_j ]);
sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
( bo_ij->BO_pi + bo_ij->BO_pi2 );
}
exp_ovun1 = p_ovun3 * exp( p_ovun4 * sum_ovun2 );
inv_exp_ovun1 = 1.0 / (1 + exp_ovun1);
Delta_lpcorr = workspace->Delta[i] -
(dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1;
exp_ovun2 = exp( p_ovun2 * Delta_lpcorr );
inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);
DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8);
CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
data->my_en.e_ov += e_ov = sum_ovun1 * CEover1;
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
(1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ));
CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 );
CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) *
p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);
/* under-coordination potential */
p_ovun2 = sbp_i->p_ovun2;
p_ovun5 = sbp_i->p_ovun5;
exp_ovun2n = 1.0 / exp_ovun2;
exp_ovun6 = exp( p_ovun6 * Delta_lpcorr );
exp_ovun8 = p_ovun7 * exp(p_ovun8 * sum_ovun2);
inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n);
inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
numbonds = 0;
e_un = 0.0;
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
numbonds ++;
if (numbonds > 0)
data->my_en.e_un += e_un =
-p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
CEunder1 = inv_exp_ovun2n *
( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
p_ovun2 * e_un * exp_ovun2n );
CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1);
CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) *
p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;
/* tally into per-atom energy */
if( system->pair_ptr->evflag) {
eng_tmp = e_ov;
if (numbonds > 0) eng_tmp += e_un;
system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
}
/* forces */
workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term
if (numbonds > 0) workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
pbond = &(bonds->select.bond_list[pj]);
j = pbond->nbr;
bo_ij = &(pbond->bo_data);
twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
[system->my_atoms[pbond->nbr].type]);
bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s;// OvCoor-1st
workspace->CdDelta[j] += CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
(bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor-3a
bo_ij->Cdbopi += CEover4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
bo_ij->Cdbopi2 += CEover4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // OvCoor-3b
workspace->CdDelta[j] += CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
(bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
bo_ij->Cdbopi += CEunder4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
bo_ij->Cdbopi2 += CEunder4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]); // UnCoor-2b
}
}
}
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 Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
double cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
far_nbrs = *lists + FAR_NBRS;
bonds = *lists + BONDS;
hbonds = *lists + HBONDS;
for( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for( i = system->n; i < system->N; ++i ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
}
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = MAX( control->hbond_cut, control->bond_cut );
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local && control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if( renbr ) {
if( nbr_pj->d <= cutoff )
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ) {
type_j = atom_j->type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
}
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local && ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
void Bonds( 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;
int type_i, type_j;
double ebond, pow_BOs_be2, exp_be12, CEbo;
double gp3, gp4, gp7, gp10, gp37;
double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
double decobdbo, decobdboua, decobdboub;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_order_data *bo_ij;
reax_list *bonds;
bonds = (*lists) + BONDS;
gp3 = system->reax_param.gp.l[3];
gp4 = system->reax_param.gp.l[4];
gp7 = system->reax_param.gp.l[7];
gp10 = system->reax_param.gp.l[10];
gp37 = (int) system->reax_param.gp.l[37];
natoms = system->n;
for( i = 0; i < natoms; ++i ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
for( pj = start_i; pj < end_i; ++pj ) {
j = bonds->select.bond_list[pj].nbr;
if( system->my_atoms[i].orig_id > system->my_atoms[j].orig_id )
continue;
if( system->my_atoms[i].orig_id == system->my_atoms[j].orig_id ) {
if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue;
if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue;
if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
system->my_atoms[j].x[1] == system->my_atoms[i].x[1] &&
system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
}
/* set the pointers */
type_i = system->my_atoms[i].type;
type_j = system->my_atoms[j].type;
sbp_i = &( system->reax_param.sbp[type_i] );
sbp_j = &( system->reax_param.sbp[type_j] );
twbp = &( system->reax_param.tbp[type_i][type_j] );
bo_ij = &( bonds->select.bond_list[pj].bo_data );
/* calculate the constants */
pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 );
exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
CEbo = -twbp->De_s * exp_be12 *
( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
/* calculate the Bond Energy */
data->my_en.e_bond += ebond =
-twbp->De_s * bo_ij->BO_s * exp_be12
-twbp->De_p * bo_ij->BO_pi
-twbp->De_pp * bo_ij->BO_pi2;
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0);
/* calculate derivatives of Bond Orders */
bo_ij->Cdbo += CEbo;
bo_ij->Cdbopi -= (CEbo + twbp->De_p);
bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
/* Stabilisation terminal triple bond */
if( bo_ij->BO >= 1.00 ) {
if( gp37 == 2 ||
(sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
(sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
hulpov = 1.0 / (1.0 + 25.0 * exphuov);
estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
data->my_en.e_bond += estriph;
decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
decobdboua = -gp10 * exphu * hulpov *
(gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
decobdboub = -gp10 * exphu * hulpov *
(gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
/* tally into per-atom energy */
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
bo_ij->Cdbo += decobdbo;
workspace->CdDelta[i] += decobdboua;
workspace->CdDelta[j] += decobdboub;
}
}
}
}
}
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
int *bond_top, int *num_3body, MPI_Comm comm )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int ihb, jhb;
int local;
double cutoff;
double r_ij;
double C12, C34, C56;
double BO, BO_s, BO_pi, BO_pi2;
reax_list *far_nbrs;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
far_nbrs = *lists + FAR_NBRS;
*Htop = 0;
memset( hb_top, 0, sizeof(int) * system->local_cap );
memset( bond_top, 0, sizeof(int) * system->total_cap );
*num_3body = 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
++(*Htop);
ihb = sbp_i->p_hbond;
}
else {
local = 0;
cutoff = control->bond_cut;
ihb = -1;
}
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if(nbr_pj->d <= cutoff) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
++(*Htop);
/* hydrogen bond lists */
if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 )
++hb_top[i];
else if( j < system->n && ihb == 2 && jhb == 1 )
++hb_top[j];
}
}
/* uncorrected bond orders */
if( nbr_pj->d <= control->bond_cut ) {
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 ) {
++bond_top[i];
++bond_top[j];
}
}
}
}
}
*Htop = (int)(MAX( *Htop * safezone, mincap * MIN_HENTRIES ));
for( i = 0; i < system->n; ++i )
hb_top[i] = (int)(MAX( hb_top[i] * saferzone, MIN_HBONDS ));
for( i = 0; i < system->N; ++i ) {
*num_3body += SQR(bond_top[i]);
bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
}
}
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 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 );
}
