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 "reaxc_torsion_angles_omp.h"
#include <mpi.h>
#include "fix_omp.h"
#include "pair_reaxc_omp.h"

#include "reaxc_defs.h"
#include "reaxc_types.h"
#include "reaxc_list.h"
#include "reaxc_vector.h"

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

#define MIN_SINE 1e-10

using namespace LAMMPS_NS;

// Functions defined in reaxc_torsion_angles.cpp
extern double Calculate_Omega(rvec, double, rvec, double, rvec, double, rvec, double,
                            three_body_interaction_data*, three_body_interaction_data*,
                            rvec, rvec, rvec, rvec, output_controls*);

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

void Torsion_AnglesOMP( reax_system *system, control_params *control,
                     simulation_data *data, storage *workspace,
                     reax_list **lists, output_controls *out_control )
{
#ifdef OMP_TIMING
  double endTimeBase, startTimeBase;
  startTimeBase = MPI_Wtime();
#endif

  int natoms = system->n;
  reax_list *bonds = (*lists) + BONDS;
  reax_list *thb_intrs = (*lists) + THREE_BODIES;
  double p_tor2 = system->reax_param.gp.l[23];
  double p_tor3 = system->reax_param.gp.l[24];
  double p_tor4 = system->reax_param.gp.l[25];
  double p_cot2 = system->reax_param.gp.l[27];
  double total_Etor = 0;
  double total_Econ = 0;
  int  nthreads = control->nthreads;

#if defined(_OPENMP)
#pragma omp parallel default(shared) reduction(+: total_Etor, total_Econ)
#endif
  {
  int i, j, k, l, pi, pj, pk, pl, pij, plk;
  int type_i, type_j, type_k, type_l;
  int start_j, end_j;
  int start_pj, end_pj, start_pk, end_pk;
  int num_frb_intrs = 0;

  double Delta_j, Delta_k;
  double r_ij, r_jk, r_kl, r_li;
  double BOA_ij, BOA_jk, BOA_kl;

  double exp_tor2_ij, exp_tor2_jk, exp_tor2_kl;
  double exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv;
  double exp_cot2_jk, exp_cot2_ij, exp_cot2_kl;
  double fn10, f11_DjDk, dfn11, fn12;
  double theta_ijk, theta_jkl;
  double sin_ijk, sin_jkl;
  double cos_ijk, cos_jkl;
  double tan_ijk_i, tan_jkl_i;
  double omega, cos_omega, cos2omega, cos3omega;
  rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl;
  double CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4;
  double CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
  double Cconj, CEconj1, CEconj2, CEconj3;
  double CEconj4, CEconj5, CEconj6;
  double e_tor, e_con;
  rvec dvec_li;
  rvec force, ext_press;
  ivec rel_box_jl;
  // rtensor total_rtensor, temp_rtensor;
  four_body_header *fbh;
  four_body_parameters *fbp;
  bond_data *pbond_ij, *pbond_jk, *pbond_kl;
  bond_order_data *bo_ij, *bo_jk, *bo_kl;
  three_body_interaction_data *p_ijk, *p_jkl;

  // Virial tallying variables
  double delil[3], deljl[3], delkl[3];
  double eng_tmp, fi_tmp[3], fj_tmp[3], fk_tmp[3];

#if defined(_OPENMP)
  int tid = omp_get_thread_num();
#else
  int tid = 0;
#endif
  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);

#if defined(_OPENMP)
#pragma omp for schedule(static)
#endif
  for (j = 0; j < system->N; ++j) {
    start_j = Start_Index(j, bonds);
    end_j = End_Index(j, bonds);

    for (pk = start_j; pk < end_j; ++pk) {
      bo_jk = &( bonds->select.bond_list[pk].bo_data );
      for (k = 0; k < nthreads; ++k)
        bo_jk->CdboReduction[k] = 0.;
    }
  }

#if defined(_OPENMP)
#pragma omp for schedule(dynamic,50)
#endif
  for (j = 0; j < natoms; ++j) {
    type_j = system->my_atoms[j].type;
    Delta_j = workspace->Delta_boc[j];
    start_j = Start_Index(j, bonds);
    end_j = End_Index(j, bonds);

    for (pk = start_j; pk < end_j; ++pk) {
      pbond_jk = &( bonds->select.bond_list[pk] );
      k = pbond_jk->nbr;
      bo_jk = &( pbond_jk->bo_data );
      BOA_jk = bo_jk->BO - control->thb_cut;

      /* see if there are any 3-body interactions involving j&k
         where j is the central atom. Otherwise there is no point in
         trying to form a 4-body interaction out of this neighborhood */
      if (system->my_atoms[j].orig_id < system->my_atoms[k].orig_id &&
          bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) {
        pj = pbond_jk->sym_index; // pj points to j on k's list

        /* do the same check as above:
           are there any 3-body interactions involving k&j
           where k is the central atom */
        if (Num_Entries(pj, thb_intrs)) {
          type_k = system->my_atoms[k].type;
          Delta_k = workspace->Delta_boc[k];
          r_jk = pbond_jk->d;

          start_pk = Start_Index(pk, thb_intrs );
          end_pk = End_Index(pk, thb_intrs );
          start_pj = Start_Index(pj, thb_intrs );
          end_pj = End_Index(pj, thb_intrs );

          exp_tor2_jk = exp( -p_tor2 * BOA_jk );
          exp_cot2_jk = exp( -p_cot2 * SQR(BOA_jk - 1.5) );
          exp_tor3_DjDk = exp( -p_tor3 * (Delta_j + Delta_k) );
          exp_tor4_DjDk = exp( p_tor4  * (Delta_j + Delta_k) );
          exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
          f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;


          /* pick i up from j-k interaction where j is the central atom */
          for (pi = start_pk; pi < end_pk; ++pi) {
            p_ijk = &( thb_intrs->select.three_body_list[pi] );
            pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
            pbond_ij = &( bonds->select.bond_list[pij] );
            bo_ij = &( pbond_ij->bo_data );

            if (bo_ij->BO > control->thb_cut/*0*/) {
              i = p_ijk->thb;
              type_i = system->my_atoms[i].type;
              r_ij = pbond_ij->d;
              BOA_ij = bo_ij->BO - control->thb_cut;

              theta_ijk = p_ijk->theta;
              sin_ijk = sin( theta_ijk );
              cos_ijk = cos( theta_ijk );
              //tan_ijk_i = 1. / tan( theta_ijk );
              if (sin_ijk >= 0 && sin_ijk <= MIN_SINE)
                tan_ijk_i = cos_ijk / MIN_SINE;
              else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
                tan_ijk_i = cos_ijk / -MIN_SINE;
              else tan_ijk_i = cos_ijk / sin_ijk;

              exp_tor2_ij = exp( -p_tor2 * BOA_ij );
              exp_cot2_ij = exp( -p_cot2 * SQR(BOA_ij -1.5) );


              /* pick l up from j-k interaction where k is the central atom */
              for (pl = start_pj; pl < end_pj; ++pl) {
                p_jkl = &( thb_intrs->select.three_body_list[pl] );
                l = p_jkl->thb;
                plk = p_jkl->pthb; //pointer to l on k's bond_list!
                pbond_kl = &( bonds->select.bond_list[plk] );
                bo_kl = &( pbond_kl->bo_data );
                type_l = system->my_atoms[l].type;
                fbh = &(system->reax_param.fbp[type_i][type_j]
                        [type_k][type_l]);
                fbp = &(system->reax_param.fbp[type_i][type_j]
                        [type_k][type_l].prm[0]);

                if (i != l && fbh->cnt &&
                    bo_kl->BO > control->thb_cut/*0*/ &&
                    bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/) {
                  ++num_frb_intrs;
                  //fprintf(stderr,
                  //      "%5d: %6d %6d %6d %6d\n", num_frb_intrs,
                  //      system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
                  //      system->my_atoms[k].orig_id,system->my_atoms[l].orig_id);

                  r_kl = pbond_kl->d;
                  BOA_kl = bo_kl->BO - control->thb_cut;

                  theta_jkl = p_jkl->theta;
                  sin_jkl = sin( theta_jkl );
                  cos_jkl = cos( theta_jkl );
                  //tan_jkl_i = 1. / tan( theta_jkl );
                  if (sin_jkl >= 0 && sin_jkl <= MIN_SINE)
                    tan_jkl_i = cos_jkl / MIN_SINE;
                  else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
                    tan_jkl_i = cos_jkl / -MIN_SINE;
                  else tan_jkl_i = cos_jkl /sin_jkl;

                  rvec_ScaledSum( dvec_li, 1., system->my_atoms[i].x,
                                  -1., system->my_atoms[l].x );
                  r_li = rvec_Norm( dvec_li );


                  /* omega and its derivative */
                  omega = Calculate_Omega( pbond_ij->dvec, r_ij,
                                           pbond_jk->dvec, r_jk,
                                           pbond_kl->dvec, r_kl,
                                           dvec_li, r_li,
                                           p_ijk, p_jkl,
                                           dcos_omega_di, dcos_omega_dj,
                                           dcos_omega_dk, dcos_omega_dl,
                                           out_control );

                  cos_omega = cos( omega );
                  cos2omega = cos( 2. * omega );
                  cos3omega = cos( 3. * omega );
                  /* end omega calculations */

                  /* torsion energy */
                  exp_tor1 = exp( fbp->p_tor1 *
                                  SQR(2.0 - bo_jk->BO_pi - f11_DjDk) );
                  exp_tor2_kl = exp( -p_tor2 * BOA_kl );
                  exp_cot2_kl = exp( -p_cot2 * SQR(BOA_kl - 1.5) );
                  fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
                    (1.0 - exp_tor2_kl);

                  CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
                               fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
                               fbp->V3 * (1.0 + cos3omega) );

                  total_Etor += e_tor = fn10 * sin_ijk * sin_jkl * CV;

                  dfn11 = (-p_tor3 * exp_tor3_DjDk +
                           (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
                           (2.0 + exp_tor3_DjDk) * exp_tor34_inv) *
                    exp_tor34_inv;

                  CEtors1 = sin_ijk * sin_jkl * CV;

                  CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
                    (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
                    sin_ijk * sin_jkl;
                  CEtors3 = CEtors2 * dfn11;

                  CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
                    (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
                  CEtors5 = CEtors1 * p_tor2 *
                    (1.0 - exp_tor2_ij) * exp_tor2_jk * (1.0 - exp_tor2_kl);
                  CEtors6 = CEtors1 * p_tor2 *
                    (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) * exp_tor2_kl;

                  cmn = -fn10 * CV;
                  CEtors7 = cmn * sin_jkl * tan_ijk_i;
                  CEtors8 = cmn * sin_ijk * tan_jkl_i;

                  CEtors9 = fn10 * sin_ijk * sin_jkl *
                    (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
                     1.5 * fbp->V3 * (cos2omega + 2.0 * SQR(cos_omega)));
                  /* end  of torsion energy */


                  /* 4-body conjugation energy */
                  fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
                  //data->my_en.e_con += e_con =
                  total_Econ += e_con =
                    fbp->p_cot1 * fn12 *
                    (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);

                  Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
                    (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);

                  CEconj1 = Cconj * (BOA_ij - 1.5e0);
                  CEconj2 = Cconj * (BOA_jk - 1.5e0);
                  CEconj3 = Cconj * (BOA_kl - 1.5e0);

                  CEconj4 = -fbp->p_cot1 * fn12 *
                    (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
                  CEconj5 = -fbp->p_cot1 * fn12 *
                    (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
                  CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
                    cos_omega * sin_ijk * sin_jkl;
                  /* end 4-body conjugation energy */

                  /* FORCES */
                  bo_jk->Cdbopi += CEtors2;
                  workspace->CdDelta[j] += CEtors3;
                  //workspace->CdDelta[k] += CEtors3;
                  workspace->CdDeltaReduction[reductionOffset+k] += CEtors3;
                  bo_ij->Cdbo += (CEtors4 + CEconj1);
                  bo_jk->Cdbo += (CEtors5 + CEconj2);
                  //bo_kl->Cdbo += (CEtors6 + CEconj3);
                  bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3);

                  if (control->virial == 0) {
                    /* dcos_theta_ijk */
                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors7 + CEconj4, p_ijk->dcos_dj );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
                                    CEtors7 + CEconj4, p_ijk->dcos_dk );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
                                    CEtors7 + CEconj4, p_ijk->dcos_di );

                    /* dcos_theta_jkl */
                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors8 + CEconj5, p_jkl->dcos_di );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
                                    CEtors8 + CEconj5, p_jkl->dcos_dj );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+l],
                                    CEtors8 + CEconj5, p_jkl->dcos_dk );

                    /* dcos_omega */
                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors9 + CEconj6, dcos_omega_dj );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i],
                                    CEtors9 + CEconj6, dcos_omega_di );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k],
                                    CEtors9 + CEconj6, dcos_omega_dk );
                    rvec_ScaledAdd( workspace->forceReduction[reductionOffset+l],
                                    CEtors9 + CEconj6, dcos_omega_dl );
                  }
                  else {
                    ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);

                    /* dcos_theta_ijk */
                    rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
                    rvec_Add( workspace->forceReduction[reductionOffset+i], force );
                    rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors7 + CEconj4, p_ijk->dcos_dj );

                    rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
                    rvec_Add( workspace->forceReduction[reductionOffset+k], force );
                    rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    /* dcos_theta_jkl */
                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors8 + CEconj5, p_jkl->dcos_di );

                    rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
                    rvec_Add( workspace->forceReduction[reductionOffset+k], force );
                    rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
                    rvec_Add( workspace->forceReduction[reductionOffset+l], force );
                    rvec_iMultiply( ext_press, rel_box_jl, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    /* dcos_omega */
                    rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
                    rvec_Add( workspace->forceReduction[reductionOffset+i], force );
                    rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    rvec_ScaledAdd( workspace->f[j],
                                    CEtors9 + CEconj6, dcos_omega_dj );

                    rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
                    rvec_Add( workspace->forceReduction[reductionOffset+k], force );
                    rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );

                    rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
                    rvec_Add( workspace->forceReduction[reductionOffset+i], force );
                    rvec_iMultiply( ext_press, rel_box_jl, force );
                    rvec_Add( workspace->my_ext_pressReduction[tid], ext_press );
                  }

                  /* tally into per-atom virials */
                  if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {

                    // acquire vectors
                    rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
                                          -1., system->my_atoms[i].x );
                    rvec_ScaledSum( deljl, 1., system->my_atoms[l].x,
                                          -1., system->my_atoms[j].x );
                    rvec_ScaledSum( delkl, 1., system->my_atoms[l].x,
                                          -1., system->my_atoms[k].x );
                    // dcos_theta_ijk
                    rvec_Scale( fi_tmp, CEtors7 + CEconj4, p_ijk->dcos_dk );
                    rvec_Scale( fj_tmp, CEtors7 + CEconj4, p_ijk->dcos_dj );
                    rvec_Scale( fk_tmp, CEtors7 + CEconj4, p_ijk->dcos_di );

                    // dcos_theta_jkl
                    rvec_ScaledAdd( fj_tmp, CEtors8 + CEconj5, p_jkl->dcos_di );
                    rvec_ScaledAdd( fk_tmp, CEtors8 + CEconj5, p_jkl->dcos_dj );

                    // dcos_omega
                    rvec_ScaledAdd( fi_tmp, CEtors9 + CEconj6, dcos_omega_di );
                    rvec_ScaledAdd( fj_tmp, CEtors9 + CEconj6, dcos_omega_dj );
                    rvec_ScaledAdd( fk_tmp, CEtors9 + CEconj6, dcos_omega_dk );

                    // tally
                    eng_tmp = e_tor + e_con;

                    if (system->pair_ptr->evflag)
                      pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, k, system->n, 1,
                                                        eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr);

                    // NEED TO MAKE AN OMP VERSION OF THIS CALL!
                    if (system->pair_ptr->vflag_atom)
                      system->pair_ptr->v_tally4(i, j, k, l, fi_tmp, fj_tmp, fk_tmp,
                                                 delil, deljl, delkl );
                  }

                } // pl check ends
              } // pl loop ends
            } // pi check ends
          } // pi loop ends
        } // k-j neighbor check ends
      } // j<k && j-k neighbor check ends
    } // pk loop ends
  } // j loop

 } // end omp parallel

  data->my_en.e_tor = total_Etor;
  data->my_en.e_con = total_Econ;

#ifdef OMP_TIMING
  endTimeBase = MPI_Wtime();
  ompTimingData[COMPUTETORSIONANGLESBOINDEX] += (endTimeBase-startTimeBase);
#endif
}