Page MenuHomec4science
Files F90415224

reaxc_multi_body.cpp
No OneTemporary
Actions

File Metadata

Created
Fri, Nov 1, 11:41

reaxc_multi_body.cpp
View Options

/*----------------------------------------------------------------------
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"
#if defined(PURE_REAX)
#include "multi_body.h"
#include "bond_orders.h"
#include "list.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_multi_body.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"
#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_lp1, p_lp2, p_lp3;
real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
real eng_tmp, f_tmp;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
bond_data *pbond;
bond_order_data *bo_ij;
reax_list *bonds = (*lists) + BONDS;
/* Initialize parameters */
p_lp1 = system->reax_param.gp.l[15];
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;
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 );
/* calculate the energy */
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];
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);
#ifdef TEST_ENERGY
// fprintf( out_control->elp, "%24.15e%24.15e%24.15e%24.15e\n",
// p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
// fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id, workspace->nlp[i],
e_lp, data->my_en.e_lp );
#endif
#ifdef TEST_FORCES
Add_dDelta( system, lists, i, CElp, workspace->f_lp ); // lp - 1st term
#endif
/* 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( !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);
#ifdef TEST_ENERGY
fprintf(out_control->elp,"C2cor%6d%6d%12.6f%12.6f%12.6f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
e_lph, deahu2dbo, deahu2dsbo );
#endif
#ifdef TEST_FORCES
Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
#endif
}
}
}
}
for( i = 0; i < system->n; ++i ) {
type_i = system->my_atoms[i].type;
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;
bo_ij = &(bonds->select.bond_list[pj].bo_data);
sbp_j = &(system->reax_param.sbp[ type_j ]);
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 );
/*fprintf( stdout, "%4d%4d%12.6f%12.6f%12.6f\n",
i+1, j+1,
dfvl * workspace->Delta_lp_temp[j],
sbp_j->nlp_opt,
workspace->nlp_temp[j] );*/
}
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);
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 + e_un;
f_tmp = CEover3 + CEunder3;
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
workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
#ifdef TEST_FORCES
Add_dDelta( system, lists, i, CEover3, workspace->f_ov ); // OvCoor 2nd
Add_dDelta( system, lists, i, CEunder3, workspace->f_un ); // UnCoor 1st
#endif
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
#ifdef TEST_ENERGY
/* fprintf( out_control->eov, "%6d%12.6f\n",
workspace->reverse_map[j],
// CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
CEover4 * (1.0 - workspace->dDelta_lp[j]) *
(bo_ij->BO_pi + bo_ij->BO_pi2)
*/// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
// fprintf( out_control->eov, "%6d%12.6f\n",
// fprintf( out_control->eov, "%6d%24.15e\n",
// system->my_atoms[j].orig_id,
// CEover1 * twbp->p_ovun1 * twbp->De_s, CEover3,
// CEover4 * (1.0 - workspace->dDelta_lp[j]) *
// (bo_ij->BO_pi + bo_ij->BO_pi2)
// /*CEover4 * (workspace->Delta[j]-workspace->Delta_lp[j])*/);
// CEunder4 * (1.0 - workspace->dDelta_lp[j]) *
// (bo_ij->BO_pi + bo_ij->BO_pi2),
// CEunder4 * (workspace->Delta[j] - workspace->Delta_lp[j]) );
#endif
#ifdef TEST_FORCES
Add_dBO( system, lists, i, pj, CEover1 * twbp->p_ovun1 * twbp->De_s,
workspace->f_ov ); // OvCoor - 1st term
Add_dDelta( system, lists, j,
CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
(bo_ij->BO_pi + bo_ij->BO_pi2),
workspace->f_ov ); // OvCoor - 3a
Add_dBOpinpi2( system, lists, i, pj,
CEover4 * (workspace->Delta[j] -
dfvl * workspace->Delta_lp_temp[j]),
CEover4 * (workspace->Delta[j] -
dfvl * workspace->Delta_lp_temp[j]),
workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
Add_dDelta( system, lists, j,
CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
(bo_ij->BO_pi + bo_ij->BO_pi2),
workspace->f_un ); // UnCoor - 2a
Add_dBOpinpi2( system, lists, i, pj,
CEunder4 * (workspace->Delta[j] -
dfvl * workspace->Delta_lp_temp[j]),
CEunder4 * (workspace->Delta[j] -
dfvl * workspace->Delta_lp_temp[j]),
workspace->f_un, workspace->f_un ); // UnCoor - 2b
#endif
}
#ifdef TEST_ENERGY
//fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
//fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
// system->my_atoms[i].orig_id, workspace->nlp[i],
// e_lp, data->my_en.e_lp );
//fprintf( out_control->eov, "%6d%24.15e%24.15e\n",
fprintf( out_control->eov, "%6d%12.4f%12.4f\n",
system->my_atoms[i].orig_id,
e_ov, data->my_en.e_ov + data->my_en.e_un );
//fprintf( out_control->eun, "%6d%24.15e%24.15e\n",
fprintf( out_control->eun, "%6d%12.4f%12.4f\n",
system->my_atoms[i].orig_id,
e_un, data->my_en.e_ov + data->my_en.e_un );
#endif
}
}

Event Timeline

c4science · Help