// clang-format off
/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "compute_snap.h"
#include "sna.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "universe.h" // For MPI

#include <cstring>

using namespace LAMMPS_NS;

enum{SCALAR,VECTOR,ARRAY};

ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
  Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snap(nullptr),
  snapall(nullptr), snap_peratom(nullptr), radelem(nullptr), wjelem(nullptr),
  sinnerelem(nullptr), dinnerelem(nullptr), snaptr(nullptr)
{

  array_flag = 1;
  extarray = 0;

  double rfac0, rmin0;
  int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;

  int ntypes = atom->ntypes;
  int nargmin = 6+2*ntypes;

  if (narg < nargmin) error->all(FLERR,"Illegal compute snap command");

  // default values

  rmin0 = 0.0;
  switchflag = 1;
  bzeroflag = 1;
  quadraticflag = 0;
  bikflag = 0;
  dgradflag = 0;
  chemflag = 0;
  bnormflag = 0;
  wselfallflag = 0;
  switchinnerflag = 0;
  nelements = 1;

  // process required arguments

  memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types
  memory->create(wjelem,ntypes+1,"snap:wjelem");
  rcutfac = atof(arg[3]);
  rfac0 = atof(arg[4]);
  twojmax = atoi(arg[5]);
  for (int i = 0; i < ntypes; i++)
    radelem[i+1] = atof(arg[6+i]);
  for (int i = 0; i < ntypes; i++)
    wjelem[i+1] = atof(arg[6+ntypes+i]);

  // construct cutsq

  double cut;
  cutmax = 0.0;
  memory->create(cutsq,ntypes+1,ntypes+1,"snap:cutsq");
  for (int i = 1; i <= ntypes; i++) {
    cut = 2.0*radelem[i]*rcutfac;
    if (cut > cutmax) cutmax = cut;
    cutsq[i][i] = cut*cut;
    for (int j = i+1; j <= ntypes; j++) {
      cut = (radelem[i]+radelem[j])*rcutfac;
      cutsq[i][j] = cutsq[j][i] = cut*cut;
    }
  }

  // set local input checks

  int sinnerflag = 0;
  int dinnerflag = 0;

  // process optional args

  int iarg = nargmin;

  while (iarg < narg) {
    if (strcmp(arg[iarg],"rmin0") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      rmin0 = atof(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      bzeroflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"switchflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      switchflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      quadraticflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"chem") == 0) {
      if (iarg+2+ntypes > narg)
        error->all(FLERR,"Illegal compute snap command");
      chemflag = 1;
      memory->create(map,ntypes+1,"compute_snap:map");
      nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
      for (int i = 0; i < ntypes; i++) {
        int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp);
        if (jelem < 0 || jelem >= nelements)
          error->all(FLERR,"Illegal compute snap command");
        map[i+1] = jelem;
      }
      iarg += 2+ntypes;
    } else if (strcmp(arg[iarg],"bnormflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      bnormflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"wselfallflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      wselfallflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"bikflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      bikflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"dgradflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      dgradflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal compute snap command");
      switchinnerflag = atoi(arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"sinner") == 0) {
      iarg++;
      if (iarg+ntypes > narg)
        error->all(FLERR,"Illegal compute snap command");
      memory->create(sinnerelem,ntypes+1,"snap:sinnerelem");
      for (int i = 0; i < ntypes; i++)
        sinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
      sinnerflag = 1;
      iarg += ntypes;
    } else if (strcmp(arg[iarg],"dinner") == 0) {
      iarg++;
      if (iarg+ntypes > narg)
        error->all(FLERR,"Illegal compute snap command");
      memory->create(dinnerelem,ntypes+1,"snap:dinnerelem");
      for (int i = 0; i < ntypes; i++)
        dinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
      dinnerflag = 1;
      iarg += ntypes;
    } else error->all(FLERR,"Illegal compute snap command");
  }

  if (switchinnerflag && !(sinnerflag && dinnerflag))
    error->all(FLERR,"Illegal compute snap command: switchinnerflag = 1, missing sinner/dinner keyword");

  if (!switchinnerflag && (sinnerflag || dinnerflag))
    error->all(FLERR,"Illegal compute snap command: switchinnerflag = 0, unexpected sinner/dinner keyword");

  if (dgradflag && !bikflag)
    error->all(FLERR,"Illegal compute snap command: dgradflag=1 requires bikflag=1");

  snaptr = new SNA(lmp, rfac0, twojmax,
                   rmin0, switchflag, bzeroflag,
                   chemflag, bnormflag, wselfallflag,
                   nelements, switchinnerflag);

  ncoeff = snaptr->ncoeff;
  nperdim = ncoeff;
  if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
  ndims_force = 3;
  ndims_virial = 6;
  yoffset = nperdim;
  zoffset = 2*nperdim;
  natoms = atom->natoms;
  bik_rows = 1;
  if (bikflag) bik_rows = natoms;
  dgrad_rows = ndims_force*natoms;
  size_array_rows = bik_rows+dgrad_rows+ndims_virial;
  if (dgradflag) size_array_cols = nperdim+3; // plus 3 for tag[i], tag[j], and cartesian index
  else size_array_cols = nperdim*atom->ntypes+1;
  lastcol = size_array_cols-1;

  ndims_peratom = ndims_force;
  size_peratom = ndims_peratom*nperdim*atom->ntypes;

  nmax = 0;
}

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

ComputeSnap::~ComputeSnap()
{

  memory->destroy(snap);
  memory->destroy(snapall);
  memory->destroy(snap_peratom);
  memory->destroy(radelem);
  memory->destroy(wjelem);
  memory->destroy(cutsq);
  delete snaptr;
  if (chemflag) memory->destroy(map);

  if (switchinnerflag) {
    memory->destroy(sinnerelem);
    memory->destroy(dinnerelem);
  }
  if (dgradflag){
    memory->destroy(dgrad);
    memory->destroy(nneighs);
    memory->destroy(neighsum);
    memory->destroy(icounter);
    memory->destroy(dbiri);
  }
}

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

void ComputeSnap::init()
{
  if (force->pair == nullptr)
    error->all(FLERR,"Compute snap requires a pair style be defined");

  if (cutmax > force->pair->cutforce){
    error->all(FLERR,"Compute snap cutoff is longer than pairwise cutoff");
  }

  // need an occasional full neighbor list

  neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);

  if (modify->get_compute_by_style("snap").size() > 1 && comm->me == 0)
    error->warning(FLERR,"More than one compute snap");
  snaptr->init();

  // allocate memory for global array

  if (dgradflag){
    // Initially allocate natoms^2 rows, will prune with neighborlist later
    memory->create(snap,natoms*natoms,ncoeff+3,
                   "snap:snap");
    memory->create(snapall,natoms*natoms,ncoeff+3,
                   "snap:snapall");
  }
  else{
    memory->create(snap,size_array_rows,size_array_cols,
                   "snap:snap");
    memory->create(snapall,size_array_rows,size_array_cols,
                   "snap:snapall");
  }
  array = snapall;

  // find compute for reference energy

  std::string id_pe = std::string("thermo_pe");
  int ipe = modify->find_compute(id_pe);
  if (ipe == -1)
    error->all(FLERR,"compute thermo_pe does not exist.");
  c_pe = modify->compute[ipe];

  // add compute for reference virial tensor
  std::string id_virial = std::string("snap_press");
  std::string pcmd = id_virial + " all pressure NULL virial";
  modify->add_compute(pcmd);

  int ivirial = modify->find_compute(id_virial);
  if (ivirial == -1)
    error->all(FLERR,"compute snap_press does not exist.");
  c_virial = modify->compute[ivirial];

}


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

void ComputeSnap::init_list(int /*id*/, NeighList *ptr)
{
  list = ptr;
}

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

void ComputeSnap::compute_array()
{

  if (dgradflag){
    get_dgrad_length();
  }

  int ntotal = atom->nlocal + atom->nghost;

  invoked_array = update->ntimestep;

  // grow snap_peratom array if necessary

  if (atom->nmax > nmax) {
    memory->destroy(snap_peratom);
    nmax = atom->nmax;
    memory->create(snap_peratom,nmax,size_peratom,
                   "snap:snap_peratom");
  }

  // clear global array
  for (int irow = 0; irow < size_array_rows; irow++){
    for (int icoeff = 0; icoeff < size_array_cols; icoeff++){
      snap[irow][icoeff] = 0.0;
    }
  }

  // clear local peratom array
  for (int i = 0; i < ntotal; i++)
    for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
      snap_peratom[i][icoeff] = 0.0;
    }

  // invoke full neighbor list (will copy or build if necessary)
  neighbor->build_one(list);

  const int inum = list->inum;
  const int* const ilist = list->ilist;
  const int* const numneigh = list->numneigh;
  int** const firstneigh = list->firstneigh;
  int * const type = atom->type;

  // compute sna derivatives for each atom in group
  // use full neighbor list to count atoms less than cutoff

  double** const x = atom->x;
  const int* const mask = atom->mask;
  int ninside;
  int numneigh_sum = 0;
  int dgrad_row_indx;
  for (int ii = 0; ii < inum; ii++) {
    int irow = 0;
    if (bikflag) irow = atom->tag[ilist[ii] & NEIGHMASK]-1;
    const int i = ilist[ii];
    if (mask[i] & groupbit) {

      const double xtmp = x[i][0];
      const double ytmp = x[i][1];
      const double ztmp = x[i][2];
      const int itype = type[i];
      int ielem = 0;
      if (chemflag)
        ielem = map[itype];
      const double radi = radelem[itype];
      const int* const jlist = firstneigh[i];
      const int jnum = numneigh[i];
      const int typeoffset_local = ndims_peratom*nperdim*(itype-1);
      const int typeoffset_global = nperdim*(itype-1);

      // insure rij, inside, and typej  are of size jnum

      snaptr->grow_rij(jnum);

      // rij[][3] = displacements between atom I and those neighbors
      // inside = indices of neighbors of I within cutoff
      // typej = types of neighbors of I within cutoff
      // note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi

      // assign quantities in snaptr

      ninside=0;
      for (int jj = 0; jj < jnum; jj++) {
        int j = jlist[jj];
        j &= NEIGHMASK;

        const double delx = x[j][0] - xtmp;
        const double dely = x[j][1] - ytmp;
        const double delz = x[j][2] - ztmp;
        const double rsq = delx*delx + dely*dely + delz*delz;
        int jtype = type[j];
        int jelem = 0;
        if (chemflag)
          jelem = map[jtype];
        if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
          snaptr->rij[ninside][0] = delx;
          snaptr->rij[ninside][1] = dely;
          snaptr->rij[ninside][2] = delz;
          snaptr->inside[ninside] = j;
          snaptr->wj[ninside] = wjelem[jtype];
          snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
          if (switchinnerflag) {
            snaptr->sinnerij[ninside] = 0.5*(sinnerelem[itype]+sinnerelem[jtype]);
            snaptr->dinnerij[ninside] = 0.5*(dinnerelem[itype]+dinnerelem[jtype]);
          }
          if (chemflag) snaptr->element[ninside] = jelem;
          ninside++;
        }
      }

      // compute bispectrum for atom i

      snaptr->compute_ui(ninside, ielem);
      snaptr->compute_zi();
      snaptr->compute_bi(ielem);

      // loop over neighbors for descriptors derivatives

      for (int jj = 0; jj < ninside; jj++) {
        const int j = snaptr->inside[jj];

        if (dgradflag){
          dgrad_row_indx = 3*neighsum[atom->tag[j]-1] + 3*icounter[atom->tag[j]-1] ;
          icounter[atom->tag[j]-1] += 1;
        }

        snaptr->compute_duidrj(jj);
        snaptr->compute_dbidrj();

        // Accumulate dBi/dRi, -dBi/dRj

        double *snadi = snap_peratom[i]+typeoffset_local;
        double *snadj = snap_peratom[j]+typeoffset_local;

        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {

          snadi[icoeff] += snaptr->dblist[icoeff][0];
          snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
          snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];

          snadj[icoeff] -= snaptr->dblist[icoeff][0];
          snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
          snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];


          if (dgradflag){
            dgrad[dgrad_row_indx+0][icoeff] = snaptr->dblist[icoeff][0];
            dgrad[dgrad_row_indx+1][icoeff] = snaptr->dblist[icoeff][1];
            dgrad[dgrad_row_indx+2][icoeff] = snaptr->dblist[icoeff][2];
            if (icoeff==(ncoeff-1)){
              dgrad[dgrad_row_indx+0][ncoeff] = atom->tag[i]-1;
              dgrad[dgrad_row_indx+0][ncoeff+1] = atom->tag[j]-1;
              dgrad[dgrad_row_indx+0][ncoeff+2] = 0;
              dgrad[dgrad_row_indx+1][ncoeff] = atom->tag[i]-1;
              dgrad[dgrad_row_indx+1][ncoeff+1] = atom->tag[j]-1;
              dgrad[dgrad_row_indx+1][ncoeff+2] = 1;
              dgrad[dgrad_row_indx+2][ncoeff] = atom->tag[i]-1;
              dgrad[dgrad_row_indx+2][ncoeff+1] = atom->tag[j]-1;
              dgrad[dgrad_row_indx+2][ncoeff+2] = 2;
            }
            // Accumulate dBi/dRi = sum (-dBi/dRj) for neighbors j of if i
            dbiri[3*(atom->tag[i]-1)+0][icoeff] -= snaptr->dblist[icoeff][0];
            dbiri[3*(atom->tag[i]-1)+1][icoeff] -= snaptr->dblist[icoeff][1];
            dbiri[3*(atom->tag[i]-1)+2][icoeff] -= snaptr->dblist[icoeff][2];
            // Get last columns which are i, j, and Cartesian index
            if (icoeff==(ncoeff-1)){
              dbiri[3*(atom->tag[i]-1)+0][ncoeff] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+0][ncoeff+1] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+0][ncoeff+2] = 0;

              dbiri[3*(atom->tag[i]-1)+1][ncoeff] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+1][ncoeff+1] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+1][ncoeff+2] = 1;

              dbiri[3*(atom->tag[i]-1)+2][ncoeff] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+2][ncoeff+1] = atom->tag[i]-1;
              dbiri[3*(atom->tag[i]-1)+2][ncoeff+2] = 2;
            }
          }


        }

        if (quadraticflag) {
          const int quadraticoffset = ncoeff;
          snadi += quadraticoffset;
          snadj += quadraticoffset;
          int ncount = 0;
          for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
            double bi = snaptr->blist[icoeff];
            double bix = snaptr->dblist[icoeff][0];
            double biy = snaptr->dblist[icoeff][1];
            double biz = snaptr->dblist[icoeff][2];

            // diagonal elements of quadratic matrix

            double dbxtmp = bi*bix;
            double dbytmp = bi*biy;
            double dbztmp = bi*biz;

            snadi[ncount] +=         dbxtmp;
            snadi[ncount+yoffset] += dbytmp;
            snadi[ncount+zoffset] += dbztmp;
            snadj[ncount] -=         dbxtmp;
            snadj[ncount+yoffset] -= dbytmp;
            snadj[ncount+zoffset] -= dbztmp;

            ncount++;

            // upper-triangular elements of quadratic matrix

            for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
              double dbxtmp = bi*snaptr->dblist[jcoeff][0]
                + bix*snaptr->blist[jcoeff];
              double dbytmp = bi*snaptr->dblist[jcoeff][1]
                + biy*snaptr->blist[jcoeff];
              double dbztmp = bi*snaptr->dblist[jcoeff][2]
                + biz*snaptr->blist[jcoeff];

              snadi[ncount] +=         dbxtmp;
              snadi[ncount+yoffset] += dbytmp;
              snadi[ncount+zoffset] += dbztmp;
              snadj[ncount] -=         dbxtmp;
              snadj[ncount+yoffset] -= dbytmp;
              snadj[ncount+zoffset] -= dbztmp;

              ncount++;
            }
          }

        }
      }

      // linear contributions
      int k;
      if (dgradflag) k = 0;
      else k = typeoffset_global;
      for (int icoeff = 0; icoeff < ncoeff; icoeff++){
        snap[irow][k++] += snaptr->blist[icoeff];
      }

      // quadratic contributions

      if (quadraticflag) {
        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
          double bveci = snaptr->blist[icoeff];
          snap[irow][k++] += 0.5*bveci*bveci;
          for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
            double bvecj = snaptr->blist[jcoeff];
            snap[irow][k++] += bveci*bvecj;
          }
        }
      }
    }

    numneigh_sum += ninside;
  } // for (int ii = 0; ii < inum; ii++)

  // Accumulate contributions to global array

  if (dgradflag){

    int dbiri_indx;
    int irow;
    for (int itype=0; itype<1; itype++){
      const int typeoffset_local = ndims_peratom*nperdim*itype;
      const int typeoffset_global = nperdim*itype;
      for (int icoeff = 0; icoeff < nperdim; icoeff++) {
        dbiri_indx=0;
        for (int i = 0; i < atom->nlocal; i++) {

            for (int jj=0; jj<nneighs[i]; jj++){

              int dgrad_row_indx = 3*neighsum[atom->tag[i]-1] + 3*jj;
              int snap_row_indx = 3*neighsum[atom->tag[i]-1] + 3*(atom->tag[i]-1) + 3*jj;
              irow = snap_row_indx + bik_rows;

              // x-coordinate
              snap[irow][icoeff+typeoffset_global] += dgrad[dgrad_row_indx+0][icoeff];
              if (icoeff==(ncoeff-1)){
                snap[irow][ncoeff] += dgrad[dgrad_row_indx+0][ncoeff];
                snap[irow][ncoeff+1] += dgrad[dgrad_row_indx+0][ncoeff+1];
                snap[irow][ncoeff+2] += dgrad[dgrad_row_indx+0][ncoeff+2];
              }
              irow++;

              // y-coordinate
              snap[irow][icoeff+typeoffset_global] += dgrad[dgrad_row_indx+1][icoeff];
              if (icoeff==(ncoeff-1)){
                snap[irow][ncoeff] += dgrad[dgrad_row_indx+1][ncoeff];
                snap[irow][ncoeff+1] += dgrad[dgrad_row_indx+1][ncoeff+1];
                snap[irow][ncoeff+2] += dgrad[dgrad_row_indx+1][ncoeff+2];
              }
              irow++;

              // z-coordinate
              snap[irow][icoeff+typeoffset_global]   += dgrad[dgrad_row_indx+2][icoeff];
              if (icoeff==(ncoeff-1)){
                snap[irow][ncoeff] += dgrad[dgrad_row_indx+2][ncoeff];
                snap[irow][ncoeff+1] += dgrad[dgrad_row_indx+2][ncoeff+1];
                snap[irow][ncoeff+2] += dgrad[dgrad_row_indx+2][ncoeff+2];
              }
              dbiri_indx = dbiri_indx+3;
            }

            // Put dBi/dRi at end of each dBj/dRi chunk.

            irow = dbiri_indx + bik_rows;

            // x-coordinate
            snap[irow][icoeff+typeoffset_global] += dbiri[3*i+0][icoeff];
            if (icoeff==(ncoeff-1)){
              snap[irow][ncoeff] += dbiri[3*i+0][ncoeff];
              snap[irow][ncoeff+1] += dbiri[3*i+0][ncoeff+1];
              snap[irow][ncoeff+2] += dbiri[3*i+0][ncoeff+2];
            }
            irow++;

            // y-coordinate
            snap[irow][icoeff+typeoffset_global] += dbiri[3*i+1][icoeff];
            if (icoeff==(ncoeff-1)){
              snap[irow][ncoeff] += dbiri[3*i+1][ncoeff];
              snap[irow][ncoeff+1] += dbiri[3*i+1][ncoeff+1];
              snap[irow][ncoeff+2] += dbiri[3*i+1][ncoeff+2];
            }
            irow++;

            // z-coordinate
            snap[irow][icoeff+typeoffset_global]   += dbiri[3*i+2][icoeff];
            if (icoeff==(ncoeff-1)){
              snap[irow][ncoeff] += dbiri[3*i+2][ncoeff];
              snap[irow][ncoeff+1] += dbiri[3*i+2][ncoeff+1];
              snap[irow][ncoeff+2] += dbiri[3*i+2][ncoeff+2];
            }

            dbiri_indx = dbiri_indx+3;
        }
      }
    }

  }

  else{

    // accumulate bispectrum force contributions to global array

    for (int itype = 0; itype < atom->ntypes; itype++) {
      const int typeoffset_local = ndims_peratom*nperdim*itype;
      const int typeoffset_global = nperdim*itype;
      for (int icoeff = 0; icoeff < nperdim; icoeff++) {
        for (int i = 0; i < ntotal; i++) {
          double *snadi = snap_peratom[i]+typeoffset_local;
          int iglobal = atom->tag[i];
          int irow = 3*(iglobal-1)+bik_rows;
          snap[irow++][icoeff+typeoffset_global] += snadi[icoeff];
          snap[irow++][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
          snap[irow][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
        }
      }
    }
  }

 // accumulate forces to global array

 if (dgradflag){
   // for dgradflag=1, put forces at last 3 columns of bik rows
   for (int i=0; i<atom->nlocal; i++){
     int iglobal = atom->tag[i];
     snap[iglobal-1][ncoeff+0] = atom->f[i][0];
     snap[iglobal-1][ncoeff+1] = atom->f[i][1];
     snap[iglobal-1][ncoeff+2] = atom->f[i][2];

   }
 }
 else{
    for (int i = 0; i < atom->nlocal; i++) {
      int iglobal = atom->tag[i];
      int irow = 3*(iglobal-1)+bik_rows;
      snap[irow++][lastcol] = atom->f[i][0];
      snap[irow++][lastcol] = atom->f[i][1];
      snap[irow][lastcol] = atom->f[i][2];
    }
  }

  // accumulate bispectrum virial contributions to global array

  if (dgradflag){
    // no virial terms for dgrad yet
  }
  else{
    dbdotr_compute();
  }

  // sum up over all processes
  MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
  // assign energy to last column
  if (dgradflag){
    // Assign reference energy right after the dgrad rows, first column.
    // Add 3N for the dBi/dRi rows.
    int irow = bik_rows + dgrad_rows + 3*natoms;
    double reference_energy = c_pe->compute_scalar();
    snapall[irow][0] = reference_energy;
  }
  else{
    for (int i = 0; i < bik_rows; i++) snapall[i][lastcol] = 0;
    int irow = 0;
    double reference_energy = c_pe->compute_scalar();
    snapall[irow][lastcol] = reference_energy;
  }

  // assign virial stress to last column
  // switch to Voigt notation

  c_virial->compute_vector();
  if (dgradflag){
    // no virial terms for dgrad yet
  }
  else{
    c_virial->compute_vector();
    int irow = 3*natoms+bik_rows;
    snapall[irow++][lastcol] = c_virial->vector[0];
    snapall[irow++][lastcol] = c_virial->vector[1];
    snapall[irow++][lastcol] = c_virial->vector[2];
    snapall[irow++][lastcol] = c_virial->vector[5];
    snapall[irow++][lastcol] = c_virial->vector[4];
    snapall[irow][lastcol] = c_virial->vector[3];
  }

}

/* ----------------------------------------------------------------------
   compute global virial contributions via summing r_i.dB^j/dr_i over
   own & ghost atoms
------------------------------------------------------------------------- */

void ComputeSnap::dbdotr_compute()
{
  double **x = atom->x;

  int irow0 = bik_rows+ndims_force*natoms;

  // sum over bispectrum contributions to forces
  // on all particles including ghosts

  int nall = atom->nlocal + atom->nghost;
  for (int i = 0; i < nall; i++)
    for (int itype = 0; itype < atom->ntypes; itype++) {
      const int typeoffset_local = ndims_peratom*nperdim*itype;
      const int typeoffset_global = nperdim*itype;
      double *snadi = snap_peratom[i]+typeoffset_local;
      for (int icoeff = 0; icoeff < nperdim; icoeff++) {
        double dbdx = snadi[icoeff];
        double dbdy = snadi[icoeff+yoffset];
        double dbdz = snadi[icoeff+zoffset];
        int irow = irow0;
        snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
        snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
        snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
        snap[irow][icoeff+typeoffset_global] += dbdy*x[i][0];
      }
    }
}

/* ----------------------------------------------------------------------
   compute dgrad length
------------------------------------------------------------------------- */

void ComputeSnap::get_dgrad_length()
{

  int rank = universe->me; // for MPI debugging

  memory->destroy(snap);
  memory->destroy(snapall);
  // invoke full neighbor list
  neighbor->build_one(list);
  dgrad_rows = 0;
  const int inum = list->inum;
  const int* const ilist = list->ilist;
  const int* const numneigh = list->numneigh;
  int** const firstneigh = list->firstneigh;
  int * const type = atom->type;
  const int* const mask = atom->mask;
  double** const x = atom->x;
  /*
  memory->create(neighsum, inum, "snap:neighsum");
  memory->create(nneighs, inum, "snap:nneighs");
  memory->create(icounter, inum, "snap:icounter");
  memory->create(dbiri, 3*atom->nlocal,ncoeff+3, "snap:dbiri");
  */
  memory->create(neighsum, natoms, "snap:neighsum");
  memory->create(nneighs, natoms, "snap:nneighs");
  memory->create(icounter, natoms, "snap:icounter");
  memory->create(dbiri, 3*natoms,ncoeff+3, "snap:dbiri");
  if (atom->nlocal != natoms){
    error->all(FLERR,"Compute snap dgradflag=1 does not support parallelism.");
  }
  for (int ii=0; ii<3*natoms; ii++){
    for (int icoeff=0; icoeff<ncoeff; icoeff++){
      dbiri[ii][icoeff]=0.0;
    }
  }
  for (int ii = 0; ii < inum; ii++) {
    const int i = ilist[ii];
    if (mask[i] & groupbit) {
      icounter[i]=0;
      neighsum[i] = 0;
      nneighs[i] = 0;
      const double xtmp = x[i][0];
      const double ytmp = x[i][1];
      const double ztmp = x[i][2];
      const int itype = type[i];
      const int* const jlist = firstneigh[i];
      const int jnum = numneigh[i];
      int jnum_cutoff = 0;
      for (int jj = 0; jj < jnum; jj++) {
        int j = jlist[jj];
        j &= NEIGHMASK;

        const double delx = x[j][0] - xtmp;
        const double dely = x[j][1] - ytmp;
        const double delz = x[j][2] - ztmp;
        const double rsq = delx*delx + dely*dely + delz*delz;
        int jtype = type[j];

        if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
          dgrad_rows += 1; //jnum + 1;
          jnum_cutoff += 1;
          nneighs[i]+=1;
        }
      }
    }
  }

  dgrad_rows *= ndims_force;

  // Loop over all atoms again to calculate neighsum.
  for (int ii = 0; ii < inum; ii++) {
    const int i = ilist[ii];
    if (mask[i] & groupbit) {
      if (i==0){
        neighsum[i]=0;
      }
      else{
        for (int jj=0; jj < ii; jj++){
          const int j = ilist[jj];
          if (mask[j] & groupbit) {
            neighsum[i] += nneighs[j];
          }
        }
      }
    }
  }

  memory->create(dgrad, dgrad_rows, ncoeff+3, "snap:dgrad");
  for (int i=0; i<dgrad_rows; i++){
    for (int j=0; j<ncoeff+3; j++){
      dgrad[i][j]=0.0;
    }
  }
  // Set size array rows which now depends on dgrad_rows.
  //size_array_rows = bik_rows+dgrad_rows+ndims_virial+3*atom->nlocal; // Add 3*N for dBi/dRi
  size_array_rows = bik_rows + dgrad_rows + 3*atom->nlocal + 1; // Add 3*N for dBi/dRi. and add 1 for reference energy

  memory->create(snap,size_array_rows,size_array_cols, "snap:snap");
  memory->create(snapall,size_array_rows,size_array_cols, "snap:snapall");
  array = snapall;

}

/* ----------------------------------------------------------------------
   compute array length
------------------------------------------------------------------------- */

double ComputeSnap::compute_scalar()
{
  if (dgradflag) get_dgrad_length();
  return size_array_rows;
}

/* ----------------------------------------------------------------------
   memory usage
------------------------------------------------------------------------- */

double ComputeSnap::memory_usage()
{

  double bytes = (double)size_array_rows*size_array_cols *
    sizeof(double);                                     // snap
  bytes += (double)size_array_rows*size_array_cols *
    sizeof(double);                                     // snapall
  bytes += (double)nmax*size_peratom * sizeof(double);  // snap_peratom
  bytes += snaptr->memory_usage();                      // SNA object
  int n = atom->ntypes+1;
  bytes += (double)n*sizeof(int);        // map

  return bytes;
}