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reaxc_bonds.cpp
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Thu, Jul 25, 10:27

reaxc_bonds.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"
#if defined(PURE_REAX)
#include "bonds.h"
#include "bond_orders.h"
#include "list.h"
#include "tool_box.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_bonds.h"
#include "reaxc_bond_orders.h"
#include "reaxc_list.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#endif
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;
real ebond, pow_BOs_be2, exp_be12, CEbo;
real gp3, gp4, gp7, gp10, gp37;
real exphu, exphua1, exphub1, exphuov, hulpov, estriph;
real 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 ) {
/* 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);
#ifdef TEST_ENERGY
//fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
system->my_atoms[i].orig_id,
system->my_atoms[j].orig_id,
bo_ij->BO, ebond, data->my_en.e_bond );
#endif
#ifdef TEST_FORCES
Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
Add_dBOpinpi2( system, lists, i, pj,
-(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
workspace->f_be, workspace->f_be );
#endif
/* 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;
#ifdef TEST_ENERGY
//fprintf( out_control->ebond,
// "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
// system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
// estriph, decobdbo, decobdboua, decobdboub );
#endif
#ifdef TEST_FORCES
Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
#endif
}
}
}
}
}
}

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