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reaxc_bond_orders.cpp
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Fri, Nov 1, 19:44

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_reax_c.h"
#include "reaxc_types.h"
#if defined(PURE_REAX)
#include "bond_orders.h"
#include "list.h"
#include "vector.h"
#include "io_tools.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
#endif
#ifdef TEST_FORCES
void Get_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
C, dBOs->select.dbo_list[k].dBO );
}
void Get_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
dbond_data *dbo_k;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
{
dbo_k = &(dBOs->select.dbo_list[k]);
rvec_Scale( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
rvec_Scale( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
}
}
void Add_dBO( reax_system *system, reax_list **lists,
int i, int pj, real C, rvec *v )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
//fprintf( stderr, "i=%d j=%d start=%d end=%d\n", i, pj, start_pj, end_pj );
for( k = start_pj; k < end_pj; ++k )
rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
C, dBOs->select.dbo_list[k].dBO );
}
void Add_dBOpinpi2( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
dbond_data *dbo_k;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
{
dbo_k = &(dBOs->select.dbo_list[k]);
rvec_ScaledAdd( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
rvec_ScaledAdd( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
}
}
void Add_dBO_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real C )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
rvec_ScaledAdd( system->my_atoms[dBOs->select.dbo_list[k].wrt].f,
C, dBOs->select.dbo_list[k].dBO );
}
void Add_dBOpinpi2_to_Forces( reax_system *system, reax_list **lists,
int i, int pj, real Cpi, real Cpi2 )
{
reax_list *bonds = (*lists) + BONDS;
reax_list *dBOs = (*lists) + DBOS;
dbond_data *dbo_k;
int start_pj, end_pj, k;
pj = bonds->select.bond_list[pj].dbond_index;
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
for( k = start_pj; k < end_pj; ++k )
{
dbo_k = &(dBOs->select.dbo_list[k]);
rvec_ScaledAdd( system->my_atoms[dbo_k->wrt].f, Cpi, dbo_k->dBOpi );
rvec_ScaledAdd( system->my_atoms[dbo_k->wrt].f, Cpi2, dbo_k->dBOpi2 );
}
}
void Add_dDelta( reax_system *system, reax_list **lists, int i, real C, rvec *v )
{
reax_list *dDeltas = &((*lists)[DDELTAS]);
int start = Start_Index(i, dDeltas);
int end = End_Index(i, dDeltas);
int k;
for( k = start; k < end; ++k )
rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
C, dDeltas->select.dDelta_list[k].dVal );
}
void Add_dDelta_to_Forces( reax_system *system, reax_list **lists,
int i, real C )
{
reax_list *dDeltas = &((*lists)[DDELTAS]);
int start = Start_Index(i, dDeltas);
int end = End_Index(i, dDeltas);
int k;
for( k = start; k < end; ++k )
rvec_ScaledAdd( system->my_atoms[dDeltas->select.dDelta_list[k].wrt].f,
C, dDeltas->select.dDelta_list[k].dVal );
}
void Calculate_dBO( int i, int pj,
storage *workspace, reax_list **lists, int *top )
{
/* Initializations */
reax_list *bonds, *dBOs;
int j, k, l, start_i, end_i, end_j;
bond_data *nbr_l, *nbr_k;
bond_order_data *bo_ij;
dbond_data *top_dbo;
// rvec due_j[1000], due_i[1000];
// rvec due_j_pi[1000], due_i_pi[1000];
// memset(due_j, 0, sizeof(rvec)*1000 );
// memset(due_i, 0, sizeof(rvec)*1000 );
// memset(due_j_pi, 0, sizeof(rvec)*1000 );
// memset(due_i_pi, 0, sizeof(rvec)*1000 );
bonds = *lists + BONDS;
dBOs = *lists + DBOS;
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
j = bonds->select.bond_list[pj].nbr;
l = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
bo_ij = &(bonds->select.bond_list[pj].bo_data);
top_dbo = &(dBOs->select.dbo_list[ (*top) ]);
for( k = start_i; k < end_i; ++k ) {
nbr_k = &(bonds->select.bond_list[k]);
for( ; l < end_j && bonds->select.bond_list[l].nbr < nbr_k->nbr; ++l ) {
/* These are the neighbors of j which are not in the nbr_list of i
Note that they might also include i! */
nbr_l = &(bonds->select.bond_list[l]);
top_dbo->wrt = nbr_l->nbr;
//rvec_ScaledAdd( due_j[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
/*3rd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp );
/*4th, dBOpp*/
rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, nbr_l->bo_data.dBOp );
if( nbr_l->nbr == i ) {
/* do the adjustments on i */
//rvec_ScaledAdd( due_i[i], bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij,
// bo_ij->dBOp ); /*1st, dBO*/
//rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
// workspace->dDeltap_self[i] ); /*2nd, dBO*/
/*1st, dBO*/
rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
/*2nd, dBO*/
rvec_ScaledAdd( top_dbo->dBO,
bo_ij->C2dbo, workspace->dDeltap_self[i] );
/*1st, dBOpi*/
rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C1dbopi,bo_ij->dln_BOp_pi );
/*2nd, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
/*3rd, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi,
bo_ij->C3dbopi, workspace->dDeltap_self[i] );
/*1st, dBO_p*/
rvec_ScaledAdd( top_dbo->dBOpi2,
bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2 );
/*2nd, dBO_p*/
rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp );
/*3rd, dBO_p*/
rvec_ScaledAdd( top_dbo->dBOpi2,
bo_ij->C3dbopi2, workspace->dDeltap_self[i] );
}
//rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
++(*top), ++top_dbo;
}
/* Now we are processing neighbor k of i. */
top_dbo->wrt = nbr_k->nbr;
//2nd, dBO
//rvec_ScaledAdd( due_i[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ij, nbr_k->bo_data.dBOp );
/*2nd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C2dbo, nbr_k->bo_data.dBOp );
/*3rd, dBOpi*/
rvec_Scale( top_dbo->dBOpi, -bo_ij->C3dbopi, nbr_k->bo_data.dBOp );
/*3rd, dBOpp*/
rvec_Scale( top_dbo->dBOpi2, -bo_ij->C3dbopi2, nbr_k->bo_data.dBOp );
if( l < end_j && bonds->select.bond_list[l].nbr == nbr_k->nbr ) {
/* This is a common neighbor of i and j. */
nbr_l = &(bonds->select.bond_list[l]);
/*3rd, dBO*/
//rvec_ScaledAdd( due_j[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
/*3rd, dBO*/
rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
rvec_ScaledAdd(top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp);
/*4th, dBOpp*/
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C4dbopi2,nbr_l->bo_data.dBOp);
++l;
}
else if( k == pj ) {
/* This negihbor is j. */
//rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij+bo_ij->BO*bo_ij->A1_ij),
// bo_ij->dBOp ); /*1st, dBO*/
//rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
// workspace->dDeltap_self[j] ); /*3rd, dBO*/
/*1st, dBO*/
rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C1dbo, bo_ij->dBOp );
/*3rd, dBO*/
rvec_ScaledAdd(top_dbo->dBO,bo_ij->C3dbo,workspace->dDeltap_self[j]);
/*1st, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
/*2nd, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C2dbopi, bo_ij->dBOp );
/*4th, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi,
bo_ij->C4dbopi, workspace->dDeltap_self[j] );
/*1st, dBOpi2*/
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C1dbopi2,bo_ij->dln_BOp_pi2);
/*2nd, dBOpi2*/
rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C2dbopi2,bo_ij->dBOp );
/*4th, dBOpi2*/
rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C4dbopi2,
workspace->dDeltap_self[j] );
}
// rvec_Add( workspace->dDelta[nbr_k->nbr], top_dbo->dBO );
++(*top), ++top_dbo;
}
for( ; l < end_j; ++l ) {
/* These are the remaining neighbors of j which are not in the
neighbor_list of i. Note that they might also include i!*/
nbr_l = &(bonds->select.bond_list[l]);
top_dbo->wrt = nbr_l->nbr;
// fprintf( stdout, "\tl: %d nbr:%d\n", l, nbr_l->nbr+1 );
// rvec_ScaledAdd( due_j[top_dbo->wrt],
// -bo_ij->BO * bo_ij->A2_ji, nbr_l->bo_data.dBOp );
/*3rd, dBO*/
rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, nbr_l->bo_data.dBOp );
/*4th, dBOpi*/
rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, nbr_l->bo_data.dBOp );
/*4th, dBOpp*/
rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, nbr_l->bo_data.dBOp );
if( nbr_l->nbr == i )
{
/* do the adjustments on i */
//rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
// bo_ij->dBOp ); /*1st, dBO*/
//rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
// workspace->dDeltap_self[i] ); /*2nd, dBO*/
/*1st, dBO*/
rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
/*2nd, dBO*/
rvec_ScaledAdd(top_dbo->dBO,bo_ij->C2dbo,workspace->dDeltap_self[i]);
/*1st, dBO_p*/
rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
/*2nd, dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp );
/*3rd,dBOpi*/
rvec_ScaledAdd( top_dbo->dBOpi,
bo_ij->C3dbopi, workspace->dDeltap_self[i] );
/*1st, dBO_p*/
rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
/*2nd, dBO_p*/
rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp);
/*3rd,dBO_p*/
rvec_ScaledAdd(top_dbo->dBOpi2,
bo_ij->C3dbopi2, workspace->dDeltap_self[i]);
}
// rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
++(*top), ++top_dbo;
}
// for( k = 0; k < 21; ++k ){
// fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
// i+1, j+1, k+1, due_i[k][0], due_i[k][1], due_i[k][2] );
// fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
// i+1, j+1, k+1, due_j[k][0], due_j[k][1], due_j[k][2] );
}
#endif
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]);
/************************************
* forces related to atom i *
* first neighbors of atom i *
************************************/
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 );
/* if( !ivec_isZero( nbr_k->rel_box ) )
fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
"ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
i+1, system->my_atoms[i].x[0],
system->my_atoms[i].x[1], system->my_atoms[i].x[2],
j+1, k+1, system->my_atoms[k].x[0],
system->my_atoms[k].x[1], system->my_atoms[k].x[2],
nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
nbr_k->rel_box[0], nbr_k->rel_box[1], nbr_k->rel_box[2],
temp[0], temp[1], temp[2] ); */
}
/* 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 );
/* ext pressure due to i is dropped, counting force on j will be enough */
/******************************************************
* forces and pressure related to atom j *
* first neighbors of atom j *
******************************************************/
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 );
/* if( !ivec_isZero( rel_box ) )
fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
"ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
i+1, j+1, system->my_atoms[j].x[0],
system->my_atoms[j].x[1], system->my_atoms[j].x[2],
k+1, system->my_atoms[k].x[0],
system->my_atoms[k].x[1], system->my_atoms[k].x[2],
nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
rel_box[0], rel_box[1], rel_box[2],
temp[0], temp[1], temp[2] ); */
}
}
/* 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 );
/* if( !ivec_isZero( nbr_j->rel_box ) )
fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]"
"ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
i+1, system->my_atoms[i].x[0], system->my_atoms[i].x[1],
system->my_atoms[i].x[2],
j+1,system->my_atoms[j].x[0], system->my_atoms[j].x[1],
system->my_atoms[j].x[2],
j+1, nbr_j->dvec[0], nbr_j->dvec[1], nbr_j->dvec[2],
nbr_j->rel_box[0], nbr_j->rel_box[1], nbr_j->rel_box[2],
temp[0], temp[1], temp[2] ); */
}
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 */
real f_scaler;
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, real 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;
real r2, C12, C34, C56;
real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
real 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 );
/* 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 -= 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;
/*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] );*/
return 1;
}
return 0;
}
int compare_bonds( const void *p1, const void *p2 )
{
return ((bond_data *)p1)->nbr - ((bond_data *)p2)->nbr;
}
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, num_bonds;
real val_i, Deltap_i, Deltap_boc_i;
real val_j, Deltap_j, Deltap_boc_j;
real f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
real exp_p1i, exp_p2i, exp_p1j, exp_p2j;
real temp, u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji;
real Cf45_ij, Cf45_ji, p_lp1; //u_ij, u_ji
real A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji;
real 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;
#ifdef TEST_FORCES
int k, pk, start_j, end_j;
int top_dbo, top_dDelta;
dbond_data *pdbo;
dDelta_data *ptop_dDelta;
reax_list *dDeltas, *dBOs;
top_dbo=0;
top_dDelta=0;
dDeltas = (*lists) + DDELTAS;
dBOs = (*lists) + DBOS;
//for( i = 0; i < system->N; ++i )
// qsort( &(bonds->select.bond_list[Start_Index(i, bonds)]),
// Num_Entries(i, bonds), sizeof(bond_data), compare_bonds );
#endif
num_bonds = 0;
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;
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;
//fprintf( stdout, "%d(%d) %24.15f\n",
// i, workspace->bond_mark[i], workspace->total_bond_order[i] );
workspace->total_bond_order[i] = 0;
}
// fprintf( stderr, "done with uncorrected bond orders\n" );
/* Corrected Bond Order calculations */
for( i = 0; i < system->N; ++i ) {
type_i = system->my_atoms[i].type;
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);
// fprintf( stderr, "i:%d Dp:%g Dbocp:%g s:%d e:%d\n",
// i+1, Deltap_i, Deltap_boc_i, start_i, end_i );
for( pj = start_i; pj < end_i; ++pj ) {
j = bonds->select.bond_list[pj].nbr;
type_j = system->my_atoms[j].type;
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] );
#ifdef TEST_FORCES
Set_Start_Index( pj, top_dbo, dBOs );
/* fprintf( stderr, "%6d%6d%12.6f%12.6f%12.6f\n",
workspace->reverse_map[i], workspace->reverse_map[j],
twbp->ovc, twbp->v13cor, bo_ij->BO ); */
#endif
if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
/* There is no correction to bond orders nor to derivatives
of bond order prime! So we leave bond orders unchanged and
set derivative of bond order coefficients such that
dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
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;
#ifdef TEST_FORCES
pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
// compute dBO_ij/dr_i
pdbo->wrt = i;
rvec_Copy( pdbo->dBO, bo_ij->dBOp );
rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
// compute dBO_ij/dr_j
pdbo++;
pdbo->wrt = j;
rvec_Scale( pdbo->dBO, -1.0, bo_ij->dBOp );
rvec_Scale( pdbo->dBOpi, -bo_ij->BO_pi, bo_ij->dln_BOp_pi );
rvec_Scale(pdbo->dBOpi2, -bo_ij->BO_pi2, bo_ij->dln_BOp_pi2);
top_dbo += 2;
#endif
}
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 ) );
/*fprintf( stderr,"%d %d\t%g %g j:%g %g p_boc:%g %g\n"
"\tf:%g %g %g, exp:%g %g %g %g\n",
i+1, j+1,
val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2,
f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
/* Now come the derivates */
/* Bond Order pages 5-7, derivative of f1 */
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 = -Cf1A_ij * p_boc1 * exp_p1i +
// Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
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 );
//fprintf( stderr, "\tCf1:%g %g\n", Cf1_ij, Cf1_ji );
}
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 */
/*temp = twbp->p_boc5 -
twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
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;
/*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f"
"A2_ij: %f A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
bo_ij->BO,
A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
/* 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;
#ifdef TEST_FORCES
Calculate_dBO( i, pj, workspace, lists, &top_dbo );
#endif
}
/* 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
/* fprintf( stderr, "%d %d\t%g %g %g %g\n"
"Cdbo:\t%g %g %g\n"
"Cdbopi:\t%g %g %g %g\n"
"Cdbopi2:%g %g %g %g\n\n",
i+1, j+1,
bonds->select.bond_list[ pj ].d,
bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
bo_ij->C1dbopi, bo_ij->C2dbopi,
bo_ij->C3dbopi, bo_ij->C4dbopi,
bo_ij->C1dbopi2,bo_ij->C2dbopi2,
bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
/* fprintf( stderr, "%d %d BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 );*/
#ifdef TEST_FORCES
Set_End_Index( pj, top_dbo, dBOs );
Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
#endif
}
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
#ifdef TEST_FORCES
Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
#endif
}
}
#ifdef TEST_FORCES
// fprintf( stderr, "dDelta computations\nj:" );
Set_Start_Index( i, top_dDelta, dDeltas );
ptop_dDelta = &( dDeltas->select.dDelta_list[top_dDelta] );
for( pj = start_i; pj < end_i; ++pj ) {
j = bonds->select.bond_list[pj].nbr;
// fprintf( stderr, "%d ", j );
if( !rvec_isZero( workspace->dDelta[j] ) ) {
ptop_dDelta->wrt = j;
rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
rvec_MakeZero( workspace->dDelta[j] );
++top_dDelta, ++ptop_dDelta;
}
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
for( pk = start_j; pk < end_j; ++pk ) {
k = bonds->select.bond_list[pk].nbr;
if( !rvec_isZero( workspace->dDelta[k] ) ) {
ptop_dDelta->wrt = k;
rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
rvec_MakeZero( workspace->dDelta[k] );
++top_dDelta, ++ptop_dDelta;
}
}
}
Set_End_Index( i, top_dDelta, dDeltas );
/*for(pj = Start_Index(i,dDeltas); pj < End_Index(i,dDeltas); ++pj)
fprintf( stdout, "dDel: %d %d [%g %g %g]\n",
i+1, dDeltas->select.dDelta_list[pj].wrt+1,
dDeltas->select.dDelta_list[pj].dVal[0],
dDeltas->select.dDelta_list[pj].dVal[1],
dDeltas->select.dDelta_list[pj].dVal[2] );*/
#endif
}
/* fprintf( stderr, "\tCalculated actual bond orders ...\n" );
fprintf( stderr, "j\tDelta\tDelta_e\tDelta_boc\tnlp"
"\tDelta_lp\tClp\tdDelta_lp\n" );
fprintf( stderr, "Atom\tDelta\t\tDelta_e\t\tDelta_boc\tnlp"
"\t\tnlp_opt\t\tDelta_lp\tClp\t\tdDelta_lp\n" );*/
p_lp1 = system->reax_param.gp.l[15];
/* Calculate some helper variables that are used at many places
throughout force calculations */
for( j = 0; j < system->N; ++j ){
type_j = system->my_atoms[j].type;
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]);
/* Adri uses different dDelta_lp values than the ones in notes... */
workspace->dDelta_lp[j] = workspace->Clp[j];
//workspace->dDelta_lp[j] = workspace->Clp[j] + (0.5-workspace->Clp[j]) *
//((fabs(workspace->Delta_e[j]/2.0 -
// (int)(workspace->Delta_e[j]/2.0)) < 0.1) ? 1 : 0 );
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];
}
//fprintf( stderr, "%d\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
//j, workspace->Delta[j], workspace->Delta_e[j], workspace->Delta_boc[j],
//workspace->nlp[j], system->reaxprm.sbp[type_j].nlp_opt,
//workspace->Delta_lp[j], workspace->Clp[j], workspace->dDelta_lp[j] );
//fprintf( stdout, "%d(%d) %24.15f\n",
// j, workspace->bond_mark[j], workspace->total_bond_order[j] );
}
//Print_Bonds( system, bonds, "pbonds.out" );
#if defined(TEST_ENERGIES) || defined(TEST_FORCES)
fprintf( stderr, "Number of bonds: %d\n", num_bonds );
Print_Bond_List( system, control, data, lists, out_control);
#endif
}
#if defined(DEPRECATED)
/* Locate j on i's list.
This function assumes that j is there for sure!
And this is the case given our method of neighbor generation*/
int Locate_Symmetric_Bond( reax_list *bonds, int i, int j )
{
int start = Start_Index(i, bonds);
int end = End_Index(i, bonds);
int mid = (start + end) / 2;
int mid_nbr;
while( (mid_nbr = bonds->select.bond_list[mid].nbr) != j ) {
/*fprintf( stderr, "\tstart: %d end: %d mid: %d\n",
start, end, mid );*/
if( mid_nbr < j )
start = mid+1;
else end = mid - 1;
mid = (start + end) / 2;
}
return mid;
}
inline void Copy_Bond_Order_Data( bond_order_data *dest, bond_order_data *src )
{
dest->BO = src->BO;
dest->BO_s = src->BO_s;
dest->BO_pi = src->BO_pi;
dest->BO_pi2 = src->BO_pi2;
rvec_Scale( dest->dBOp, -1.0, src->dBOp );
rvec_Scale( dest->dln_BOp_s, -1.0, src->dln_BOp_s );
rvec_Scale( dest->dln_BOp_pi, -1.0, src->dln_BOp_pi );
rvec_Scale( dest->dln_BOp_pi2, -1.0, src->dln_BOp_pi2 );
}
#endif

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