139 lines
5.3 KiB
C++
139 lines
5.3 KiB
C++
/*----------------------------------------------------------------------
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PuReMD - Purdue ReaxFF Molecular Dynamics Program
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Copyright (2010) Purdue University
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Hasan Metin Aktulga, hmaktulga@lbl.gov
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Joseph Fogarty, jcfogart@mail.usf.edu
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Sagar Pandit, pandit@usf.edu
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Ananth Y Grama, ayg@cs.purdue.edu
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Please cite the related publication:
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H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
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"Parallel Reactive Molecular Dynamics: Numerical Methods and
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Algorithmic Techniques", Parallel Computing, in press.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License as
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published by the Free Software Foundation; either version 2 of
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the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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See the GNU General Public License for more details:
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<http://www.gnu.org/licenses/>.
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----------------------------------------------------------------------*/
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#include "pair_reaxc.h"
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#include "reaxc_bonds.h"
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#include "reaxc_bond_orders.h"
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#include "reaxc_list.h"
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#include "reaxc_tool_box.h"
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#include "reaxc_vector.h"
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void Bonds( reax_system *system, control_params * /*control*/,
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simulation_data *data, storage *workspace, reax_list **lists,
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output_controls * /*out_control*/ )
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{
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int i, j, pj, natoms;
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int start_i, end_i;
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int type_i, type_j;
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double ebond, pow_BOs_be2, exp_be12, CEbo;
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double gp3, gp4, gp7, gp10, gp37;
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double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
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double decobdbo, decobdboua, decobdboub;
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single_body_parameters *sbp_i, *sbp_j;
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two_body_parameters *twbp;
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bond_order_data *bo_ij;
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reax_list *bonds;
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bonds = (*lists) + BONDS;
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gp3 = system->reax_param.gp.l[3];
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gp4 = system->reax_param.gp.l[4];
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gp7 = system->reax_param.gp.l[7];
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gp10 = system->reax_param.gp.l[10];
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gp37 = (int) system->reax_param.gp.l[37];
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natoms = system->n;
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for( i = 0; i < natoms; ++i ) {
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start_i = Start_Index(i, bonds);
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end_i = End_Index(i, bonds);
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for( pj = start_i; pj < end_i; ++pj ) {
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j = bonds->select.bond_list[pj].nbr;
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if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id)
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continue;
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if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) {
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if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue;
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if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
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system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue;
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if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
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system->my_atoms[j].x[1] == system->my_atoms[i].x[1] &&
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system->my_atoms[j].x[0] < system->my_atoms[i].x[0]) continue;
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}
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/* set the pointers */
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type_i = system->my_atoms[i].type;
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type_j = system->my_atoms[j].type;
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sbp_i = &( system->reax_param.sbp[type_i] );
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sbp_j = &( system->reax_param.sbp[type_j] );
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twbp = &( system->reax_param.tbp[type_i][type_j] );
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bo_ij = &( bonds->select.bond_list[pj].bo_data );
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/* calculate the constants */
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if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0;
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else pow_BOs_be2 = pow( bo_ij->BO_s, twbp->p_be2 );
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exp_be12 = exp( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
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CEbo = -twbp->De_s * exp_be12 *
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( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
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/* calculate the Bond Energy */
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data->my_en.e_bond += ebond =
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-twbp->De_s * bo_ij->BO_s * exp_be12
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-twbp->De_p * bo_ij->BO_pi
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-twbp->De_pp * bo_ij->BO_pi2;
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/* tally into per-atom energy */
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if (system->pair_ptr->evflag)
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system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0);
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/* calculate derivatives of Bond Orders */
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bo_ij->Cdbo += CEbo;
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bo_ij->Cdbopi -= (CEbo + twbp->De_p);
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bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
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/* Stabilisation terminal triple bond */
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if (bo_ij->BO >= 1.00) {
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if( gp37 == 2 ||
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(sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
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(sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
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exphu = exp( -gp7 * SQR(bo_ij->BO - 2.50) );
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exphua1 = exp(-gp3 * (workspace->total_bond_order[i]-bo_ij->BO));
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exphub1 = exp(-gp3 * (workspace->total_bond_order[j]-bo_ij->BO));
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exphuov = exp(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
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hulpov = 1.0 / (1.0 + 25.0 * exphuov);
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estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
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data->my_en.e_bond += estriph;
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decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
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( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
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decobdboua = -gp10 * exphu * hulpov *
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(gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
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decobdboub = -gp10 * exphu * hulpov *
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(gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
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/* tally into per-atom energy */
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if (system->pair_ptr->evflag)
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system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
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bo_ij->Cdbo += decobdbo;
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workspace->CdDelta[i] += decobdboua;
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workspace->CdDelta[j] += decobdboub;
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}
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}
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}
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}
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}
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