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reaxc_bond_orders.cpp
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Sun, Jun 30, 22:42

reaxc_bond_orders.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reaxc.h"
#include "reaxc_types.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data,
storage *workspace, reax_list **lists )
{
reax_list *bonds = (*lists) + BONDS;
bond_data *nbr_j, *nbr_k;
bond_order_data *bo_ij, *bo_ji;
dbond_coefficients coef;
rvec temp, ext_press;
ivec rel_box;
int pk, k, j;
/* Initializations */
nbr_j = &(bonds->select.bond_list[pj]);
j = nbr_j->nbr;
bo_ij = &(nbr_j->bo_data);
bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
rvec_Scale(temp, -coef.C2dbo, nbr_k->bo_data.dBOp); /*2nd, dBO*/
rvec_ScaledAdd(temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
rvec_ScaledAdd(temp, -coef.C3dbopi, nbr_k->bo_data.dBOp); /*3rd, dBOpi*/
rvec_ScaledAdd(temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);/*3rd, dBOpi2*/
/* force */
rvec_Add( workspace->f[k], temp );
/* pressure */
rvec_iMultiply( ext_press, nbr_k->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
/* then atom i itself */
rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st,dBO*/
rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd,dBO*/
rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st,dBO*/
rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd,dBO*/
rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);/*3rd,dBOpi*/
rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBO_pi2*/
rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );/*3rd*/
/* force */
rvec_Add( workspace->f[i], temp );
for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
nbr_k = &(bonds->select.bond_list[pk]);
k = nbr_k->nbr;
rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/
rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);/*dDelta*/
rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp); /*4th,dBOpi*/
rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);/*4th,dBOpi2*/
/* force */
rvec_Add( workspace->f[k], temp );
/* pressure */
if( k != i ) {
ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i)
rvec_iMultiply( ext_press, rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
}
/* then atom j itself */
rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/
rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);/*2nd, dBO*/
rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);/*3rd,dBOpi*/
rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 ); /*1st,dBOpi2*/
rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp ); /*2nd,dBOpi2*/
rvec_ScaledAdd( temp,coef.C4dbopi2,workspace->dDeltap_self[j]);/*3rd,dBOpi2*/
/* force */
rvec_Add( workspace->f[j], temp );
/* pressure */
rvec_iMultiply( ext_press, nbr_j->rel_box, temp );
rvec_Add( data->my_ext_press, ext_press );
}
void Add_dBond_to_Forces( reax_system *system, int i, int pj,
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;
int pk, k, j;
/* Virial Tallying variables */
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
/* 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]);
// forces on i
rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] );
rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );
rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi );
rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i]);
rvec_ScaledAdd( temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
rvec_ScaledAdd( temp, coef.C2dbopi2, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] );
rvec_Add( workspace->f[i], temp );
if( system->pair_ptr->vflag_atom) {
rvec_Scale(fi_tmp, -1.0, temp);
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x );
system->pair_ptr->v_tally(i,fi_tmp,delij);
}
// forces on j
rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] );
rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j]);
rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi );
rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j]);
rvec_ScaledAdd( temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
rvec_ScaledAdd( temp, -coef.C2dbopi2, bo_ij->dBOp );
rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]);
rvec_Add( workspace->f[j], temp );
if( system->pair_ptr->vflag_atom) {
rvec_Scale(fj_tmp, -1.0, temp);
rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x );
system->pair_ptr->v_tally(j,fj_tmp,delji);
}
// forces on k: i neighbor
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);
rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp);
rvec_Add( workspace->f[k], temp );
if( system->pair_ptr->vflag_atom ) {
rvec_Scale(fk_tmp, -1.0, temp);
rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x);
system->pair_ptr->v_tally(k,fk_tmp,delki);
rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x);
system->pair_ptr->v_tally(k,fk_tmp,delkj);
}
}
// forces on k: j neighbor
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 );
rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp);
rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp);
rvec_Add( workspace->f[k], temp );
if( system->pair_ptr->vflag_atom ) {
rvec_Scale(fk_tmp, -1.0, temp);
rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x);
system->pair_ptr->v_tally(k,fk_tmp,delki);
rvec_ScaledSum(delkj,1.,system->my_atoms[k].x,-1.,system->my_atoms[j].x);
system->pair_ptr->v_tally(k,fk_tmp,delkj);
}
}
}
int BOp( storage *workspace, reax_list *bonds, double bo_cut,
int i, int btop_i, far_neighbor_data *nbr_pj,
single_body_parameters *sbp_i, single_body_parameters *sbp_j,
two_body_parameters *twbp ) {
int j, btop_j;
double r2, C12, C34, C56;
double Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
double BO, BO_s, BO_pi, BO_pi2;
bond_data *ibond, *jbond;
bond_order_data *bo_ij, *bo_ji;
j = nbr_pj->nbr;
r2 = SQR(nbr_pj->d);
if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) {
C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 );
BO_s = (1.0 + bo_cut) * exp( C12 );
}
else BO_s = C12 = 0.0;
if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) {
C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 );
BO_pi = exp( C34 );
}
else BO_pi = C34 = 0.0;
if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) {
C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 );
BO_pi2= exp( C56 );
}
else BO_pi2 = C56 = 0.0;
/* Initially BO values are the uncorrected ones, page 1 */
BO = BO_s + BO_pi + BO_pi2;
if( BO >= bo_cut ) {
/****** bonds i-j and j-i ******/
ibond = &( bonds->select.bond_list[btop_i] );
btop_j = End_Index( j, bonds );
jbond = &(bonds->select.bond_list[btop_j]);
ibond->nbr = j;
jbond->nbr = i;
ibond->d = nbr_pj->d;
jbond->d = nbr_pj->d;
rvec_Copy( ibond->dvec, nbr_pj->dvec );
rvec_Scale( jbond->dvec, -1, nbr_pj->dvec );
ivec_Copy( ibond->rel_box, nbr_pj->rel_box );
ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box );
ibond->dbond_index = btop_i;
jbond->dbond_index = btop_i;
ibond->sym_index = btop_j;
jbond->sym_index = btop_i;
Set_End_Index( j, btop_j+1, bonds );
bo_ij = &( ibond->bo_data );
bo_ji = &( jbond->bo_data );
bo_ji->BO = bo_ij->BO = BO;
bo_ji->BO_s = bo_ij->BO_s = BO_s;
bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
/* Bond Order page2-3, derivative of total bond order prime */
Cln_BOp_s = twbp->p_bo2 * C12 / r2;
Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
/* Only dln_BOp_xx wrt. dr_i is stored here, note that
dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec);
rvec_Scale(bo_ij->dln_BOp_pi2,
-bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
rvec_Scale( bo_ij->dBOp,
-(bo_ij->BO_s * Cln_BOp_s +
bo_ij->BO_pi * Cln_BOp_pi +
bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
bo_ij->BO_s -= bo_cut;
bo_ij->BO -= bo_cut;
bo_ji->BO_s -= bo_cut;
bo_ji->BO -= bo_cut;
workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
return 1;
}
return 0;
}
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];
}
}
}

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