lammps-sys 0.6.0

/*----------------------------------------------------------------------
  PuReMD - Purdue ReaxFF Molecular Dynamics Program
  Website: https://www.cs.purdue.edu/puremd

  Copyright (2010) Purdue University

  Contributing authors:
  H. M. Aktulga, J. Fogarty, S. Pandit, A. Grama
  Corresponding author:
  Hasan Metin Aktulga, Michigan State University, hma@cse.msu.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, 38 (4-5), 245-259

  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_reaxc_omp.h"
#include "thr_data.h"

#include "reaxc_defs.h"
#include "reaxc_types.h"

#include "reaxc_nonbonded.h"
#include "reaxc_nonbonded_omp.h"
#include "reaxc_bond_orders_omp.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"

#if defined(_OPENMP)
#include  <omp.h>
#endif

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
                             simulation_data *data, storage *workspace,
                             reax_list **lists, output_controls * /* out_control */ )
{
  int natoms = system->n;
  reax_list *far_nbrs = (*lists) + FAR_NBRS;
  double p_vdW1 = system->reax_param.gp.l[28];
  double p_vdW1i = 1.0 / p_vdW1;
  double total_EvdW = 0.;
  double total_Eele = 0.;

#if defined(_OPENMP)
#pragma omp parallel default(shared) reduction(+: total_EvdW, total_Eele)
#endif
  {
#if defined(_OPENMP)
    int tid = omp_get_thread_num();
#else
    int tid = 0;
#endif
  int i, j, pj;
  int start_i, end_i, orig_i, orig_j, flag;
  double powr_vdW1, powgi_vdW1;
  double tmp, r_ij, fn13, exp1, exp2;
  double Tap, dTap, dfn13, CEvd, CEclmb, de_core;
  double dr3gamij_1, dr3gamij_3;
  double e_ele, e_vdW, e_core;
  const double SMALL = 0.0001;
  double e_lg, de_lg, r_ij5, r_ij6, re6;
  rvec temp, ext_press;
  two_body_parameters *twbp;
  far_neighbor_data *nbr_pj;

  // Tallying variables:
  double pe_vdw, f_tmp, delij[3];

  long reductionOffset = (system->N * tid);

  class PairReaxCOMP *pair_reax_ptr;
  pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
  class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);

  e_core = 0;
  e_vdW = 0;
  e_lg = 0;
  de_lg = 0.0;

#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
  for( i = 0; i < natoms; ++i ) {
    if(system->my_atoms[i].type < 0) continue;
    start_i = Start_Index(i, far_nbrs);
    end_i   = End_Index(i, far_nbrs);
    orig_i  = system->my_atoms[i].orig_id;

    for( pj = start_i; pj < end_i; ++pj ) {
      nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
      j = nbr_pj->nbr;
      orig_j  = system->my_atoms[j].orig_id;

      flag = 0;
      if(nbr_pj->d <= control->nonb_cut) {
        if(j < natoms) flag = 1;
        else if (orig_i < orig_j) flag = 1;
        else if (orig_i == orig_j) {
          if (nbr_pj->dvec[2] > SMALL) flag = 1;
          else if (fabs(nbr_pj->dvec[2]) < SMALL) {
            if (nbr_pj->dvec[1] > SMALL) flag = 1;
            else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
              flag = 1;
          }
        }
      }

      if (flag) {

        r_ij = nbr_pj->d;
        twbp = &(system->reax_param.tbp[ system->my_atoms[i].type ]
                 [ system->my_atoms[j].type ]);

        /* Calculate Taper and its derivative */
        // Tap = nbr_pj->Tap;   -- precomputed during compte_H
        Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
        Tap = Tap * r_ij + workspace->Tap[5];
        Tap = Tap * r_ij + workspace->Tap[4];
        Tap = Tap * r_ij + workspace->Tap[3];
        Tap = Tap * r_ij + workspace->Tap[2];
        Tap = Tap * r_ij + workspace->Tap[1];
        Tap = Tap * r_ij + workspace->Tap[0];

        dTap = 7*workspace->Tap[7] * r_ij + 6*workspace->Tap[6];
        dTap = dTap * r_ij + 5*workspace->Tap[5];
        dTap = dTap * r_ij + 4*workspace->Tap[4];
        dTap = dTap * r_ij + 3*workspace->Tap[3];
        dTap = dTap * r_ij + 2*workspace->Tap[2];
        dTap += workspace->Tap[1]/r_ij;

        /*vdWaals Calculations*/
        if(system->reax_param.gp.vdw_type==1 || system->reax_param.gp.vdw_type==3)
          { // shielding
            powr_vdW1 = pow(r_ij, p_vdW1);
            powgi_vdW1 = pow( 1.0 / twbp->gamma_w, p_vdW1);

            fn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i );
            exp1 = exp( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
            exp2 = exp( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );

            e_vdW = twbp->D * (exp1 - 2.0 * exp2);
            total_EvdW += Tap * e_vdW;

            dfn13 = pow( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
              pow(r_ij, p_vdW1 - 2.0);

            CEvd = dTap * e_vdW -
              Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
          }
        else { // no shielding
          exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
          exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );

          e_vdW = twbp->D * (exp1 - 2.0 * exp2);
          total_EvdW += Tap * e_vdW;

          CEvd = dTap * e_vdW -
              Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) / r_ij;
        }

        if(system->reax_param.gp.vdw_type==2 || system->reax_param.gp.vdw_type==3)
          { // innner wall
            e_core = twbp->ecore * exp(twbp->acore * (1.0-(r_ij/twbp->rcore)));
            total_EvdW += Tap * e_core;

            de_core = -(twbp->acore/twbp->rcore) * e_core;
            CEvd += dTap * e_core + Tap * de_core / r_ij;

            //  lg correction, only if lgvdw is yes
            if (control->lgflag) {
              r_ij5 = pow( r_ij, 5.0 );
              r_ij6 = pow( r_ij, 6.0 );
              re6 = pow( twbp->lgre, 6.0 );

              e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
              total_EvdW += Tap * e_lg;

              de_lg = -6.0 * e_lg *  r_ij5 / ( r_ij6 + re6 ) ;
              CEvd += dTap * e_lg + Tap * de_lg / r_ij;
            }

          }

        /*Coulomb Calculations*/
        dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
        dr3gamij_3 = pow( dr3gamij_1 , 0.33333333333333 );

        tmp = Tap / dr3gamij_3;
        total_Eele += e_ele =
          C_ele * system->my_atoms[i].q * system->my_atoms[j].q * tmp;

        CEclmb = C_ele * system->my_atoms[i].q * system->my_atoms[j].q *
          ( dTap -  Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;

        /* tally into per-atom energy */
        if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
          pe_vdw = Tap * (e_vdW + e_core + e_lg);
          rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
                          -1., system->my_atoms[j].x );
          f_tmp = -(CEvd + CEclmb);
          pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms,
                                            1, pe_vdw, e_ele, f_tmp,
                                            delij[0], delij[1], delij[2], thr);
        }

        if (control->virial == 0) {
          rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
          rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j],
                          +(CEvd + CEclmb), nbr_pj->dvec );
        } else { /* NPT, iNPT or sNPT */
          /* for pressure coupling, terms not related to bond order
             derivatives are added directly into pressure vector/tensor */

          rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
          rvec_ScaledAdd( workspace->f[reductionOffset+i], -1., temp );
          rvec_Add( workspace->forceReduction[reductionOffset+j], temp);

          rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );

          rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
        }
        }
      }
    }

  pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either,
                                  system->pair_ptr->vflag_either, thr);
  } // parallel region

  data->my_en.e_vdW = total_EvdW;
  data->my_en.e_ele = total_Eele;

  Compute_Polarization_Energy( system, data );
}

/* ---------------------------------------------------------------------- */

void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control,
                                      simulation_data *data, storage *workspace,
                                      reax_list **lists,
                                      output_controls * /* out_control */) {

  double SMALL = 0.0001;
  int  natoms = system->n;
  reax_list *far_nbrs = (*lists) + FAR_NBRS;
  double total_EvdW = 0.;
  double total_Eele = 0.;

#if defined(_OPENMP)
#pragma omp parallel default(shared) reduction(+:total_EvdW, total_Eele)
#endif
  {
  int i, j, pj, r;
  int type_i, type_j, tmin, tmax;
  int start_i, end_i, orig_i, orig_j, flag;
  double r_ij, base, dif;
  double e_vdW, e_ele;
  double CEvd, CEclmb;
  double f_tmp, delij[3];
  rvec temp, ext_press;
  far_neighbor_data *nbr_pj;
  LR_lookup_table *t;
#if defined(_OPENMP)
  int tid = omp_get_thread_num();
  #else
  int tid = 0;
#endif
  long froffset = (system->N * tid);
  LR_lookup_table ** & LR = system->LR;

  class PairReaxCOMP *pair_reax_ptr;
  pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
  class ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);

#if defined(_OPENMP)
#pragma omp for schedule(guided)
#endif
  for (i = 0; i < natoms; ++i) {
    type_i  = system->my_atoms[i].type;
    if(type_i < 0) continue;
    start_i = Start_Index(i,far_nbrs);
    end_i   = End_Index(i,far_nbrs);
    orig_i  = system->my_atoms[i].orig_id;

    for (pj = start_i; pj < end_i; ++pj) {
      nbr_pj = &(far_nbrs->select.far_nbr_list[pj]);
      j = nbr_pj->nbr;
      type_j = system->my_atoms[j].type;
      if(type_j < 0) continue;
      orig_j  = system->my_atoms[j].orig_id;

      flag = 0;
      if(nbr_pj->d <= control->nonb_cut) {
        if(j < natoms) flag = 1;
        else if (orig_i < orig_j) flag = 1;
        else if (orig_i == orig_j) {
          if (nbr_pj->dvec[2] > SMALL) flag = 1;
          else if (fabs(nbr_pj->dvec[2]) < SMALL) {
            if (nbr_pj->dvec[1] > SMALL) flag = 1;
            else if (fabs(nbr_pj->dvec[1]) < SMALL && nbr_pj->dvec[0] > SMALL)
              flag = 1;
          }
        }

      }

      if (flag) {

        r_ij   = nbr_pj->d;
        tmin  = MIN( type_i, type_j );
        tmax  = MAX( type_i, type_j );
        t = &( LR[tmin][tmax] );

        /* Cubic Spline Interpolation */
        r = (int)(r_ij * t->inv_dx);
        if (r == 0)  ++r;
        base = (double)(r+1) * t->dx;
        dif = r_ij - base;

        e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
          t->vdW[r].a;

        e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
          t->ele[r].a;
        e_ele *= system->my_atoms[i].q * system->my_atoms[j].q;

        total_EvdW += e_vdW;
        total_Eele += e_ele;

        CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
          t->CEvd[r].a;

        CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
          t->CEclmb[r].a;
        CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q;

        /* tally into per-atom energy */
        if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
          rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
                          -1., system->my_atoms[j].x );
          f_tmp = -(CEvd + CEclmb);
          pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, natoms, 1, e_vdW, e_ele,
                                            f_tmp, delij[0], delij[1], delij[2], thr);
        }

        if (control->virial == 0) {
          rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec );
          rvec_ScaledAdd( workspace->forceReduction[froffset+j],
                          +(CEvd + CEclmb), nbr_pj->dvec );
        } else { // NPT, iNPT or sNPT
          /* for pressure coupling, terms not related to bond order derivatives
             are added directly into pressure vector/tensor */
          rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );

          rvec_ScaledAdd( workspace->f[i], -1., temp );
          rvec_Add( workspace->forceReduction[froffset+j], temp );

          rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
          rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
        }
      }
    }
  }

  pair_reax_ptr->reduce_thr_proxy(system->pair_ptr, system->pair_ptr->eflag_either,
                                  system->pair_ptr->vflag_either, thr);
  } // end omp parallel

  data->my_en.e_vdW = total_EvdW;
  data->my_en.e_ele = total_Eele;

  Compute_Polarization_Energy( system, data );
}