/*----------------------------------------------------------------------
  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
          }
        }
      }
    }
  }
}
