lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
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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 "reaxc_bonds.h"
#include <cmath>
#include "pair.h"
#include "reaxc_defs.h"
#include "reaxc_list.h"

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;
  double ebond, pow_BOs_be2, exp_be12, CEbo;
  double gp3, gp4, gp7, gp10, gp37;
  double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
  double 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)
        continue;
      if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) {
        if (system->my_atoms[j].x[2] <  system->my_atoms[i].x[2]) continue;
        if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
            system->my_atoms[j].x[1] <  system->my_atoms[i].x[1]) continue;
        if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] &&
            system->my_atoms[j].x[1] == system->my_atoms[i].x[1] &&
            system->my_atoms[j].x[0] <  system->my_atoms[i].x[0]) continue;
      }

      /* 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 */
      if (bo_ij->BO_s == 0.0) pow_BOs_be2 = 0.0;
      else 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);

      /* 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;
        }
      }
    }
  }
}