/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, 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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */

#include <cstdlib>
#include "atom_vec_dpd.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

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

AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp)
{
  molecular = 0;
  mass_type = 1;

  comm_x_only = comm_f_only = 0; // we communicate not only x forward but also dpdTheta
  size_forward = 7; // 3 + dpdTheta + uCond + uMech + uChem
  size_reverse = 3; // 3
  size_border = 12; // 6 + dpdTheta + uCond + uMech + uChem + uCG + uCGnew
  size_velocity = 3;
  size_data_atom = 6; // we read id + type + dpdTheta + x + y + z
  size_data_vel = 4;
  xcol_data = 4; // 1=id 2=type 3=dpdTheta 4=x

  atom->rho_flag = 1;
  atom->dpd_flag = 1;
}

/* ----------------------------------------------------------------------
   grow atom arrays
   n = 0 grows arrays by a chunk
   n > 0 allocates arrays to size n
------------------------------------------------------------------------- */

void AtomVecDPD::grow(int n)
{
  if (n == 0) grow_nmax();
  else nmax = n;
  atom->nmax = nmax;
  if (nmax < 0)
    error->one(FLERR,"Per-processor system is too big");

  tag = memory->grow(atom->tag,nmax,"atom:tag");
  type = memory->grow(atom->type,nmax,"atom:type");
  mask = memory->grow(atom->mask,nmax,"atom:mask");
  image = memory->grow(atom->image,nmax,"atom:image");
  x = memory->grow(atom->x,nmax,3,"atom:x");
  v = memory->grow(atom->v,nmax,3,"atom:v");
  f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");

  rho = memory->grow(atom->rho, nmax, "atom:rho");
  dpdTheta = memory->grow(atom->dpdTheta, nmax, "atom:dpdTheta");
  uCond = memory->grow(atom->uCond,nmax,"atom:uCond");
  uMech = memory->grow(atom->uMech,nmax,"atom:uMech");
  uChem = memory->grow(atom->uChem,nmax,"atom:uChem");
  uCG = memory->grow(atom->uCG,nmax,"atom:uCG");
  uCGnew = memory->grow(atom->uCGnew,nmax,"atom:uCGnew");
  duChem = memory->grow(atom->duChem,nmax,"atom:duChem");

  if (atom->nextra_grow)
    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
      modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}

/* ----------------------------------------------------------------------
   reset local array ptrs
------------------------------------------------------------------------- */

void AtomVecDPD::grow_reset()
{
  tag = atom->tag; type = atom->type;
  mask = atom->mask; image = atom->image;
  x = atom->x; v = atom->v; f = atom->f;
  rho = atom->rho;
  dpdTheta = atom->dpdTheta;
  uCond = atom->uCond;
  uMech = atom->uMech;
  uChem = atom->uChem;
  uCG = atom->uCG;
  uCGnew = atom->uCGnew;
  duChem = atom->duChem;
}

/* ----------------------------------------------------------------------
   copy atom I info to atom J
------------------------------------------------------------------------- */

void AtomVecDPD::copy(int i, int j, int delflag)
{
  tag[j] = tag[i];
  type[j] = type[i];
  mask[j] = mask[i];
  image[j] = image[i];
  x[j][0] = x[i][0];
  x[j][1] = x[i][1];
  x[j][2] = x[i][2];
  v[j][0] = v[i][0];
  v[j][1] = v[i][1];
  v[j][2] = v[i][2];
  dpdTheta[j] = dpdTheta[i];
  uCond[j] = uCond[i];
  uMech[j] = uMech[i];
  uChem[j] = uChem[i];
  uCG[j] = uCG[i];
  uCGnew[j] = uCGnew[i];

  if (atom->nextra_grow)
    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
}

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

int AtomVecDPD::pack_comm(int n, int *list, double *buf,
                             int pbc_flag, int *pbc)
{
  int i,j,m;
  double dx,dy,dz;

  m = 0;
  if (pbc_flag == 0) {
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0];
      buf[m++] = x[j][1];
      buf[m++] = x[j][2];
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
    }
  } else {
    if (domain->triclinic == 0) {
      dx = pbc[0]*domain->xprd;
      dy = pbc[1]*domain->yprd;
      dz = pbc[2]*domain->zprd;
    } else {
      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
      dz = pbc[2]*domain->zprd;
    }
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0] + dx;
      buf[m++] = x[j][1] + dy;
      buf[m++] = x[j][2] + dz;
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
    }
  }
  return m;
}

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

int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf,
                                 int pbc_flag, int *pbc)
{
  int i,j,m;
  double dx,dy,dz,dvx,dvy,dvz;

  m = 0;
  if (pbc_flag == 0) {
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0];
      buf[m++] = x[j][1];
      buf[m++] = x[j][2];
      buf[m++] = v[j][0];
      buf[m++] = v[j][1];
      buf[m++] = v[j][2];
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
    }
  } else {
    if (domain->triclinic == 0) {
      dx = pbc[0]*domain->xprd;
      dy = pbc[1]*domain->yprd;
      dz = pbc[2]*domain->zprd;
    } else {
      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
      dz = pbc[2]*domain->zprd;
    }
    if (!deform_vremap) {
      for (i = 0; i < n; i++) {
        j = list[i];
        buf[m++] = x[j][0] + dx;
        buf[m++] = x[j][1] + dy;
        buf[m++] = x[j][2] + dz;
        buf[m++] = v[j][0];
        buf[m++] = v[j][1];
        buf[m++] = v[j][2];
        buf[m++] = dpdTheta[j];
        buf[m++] = uCond[j];
        buf[m++] = uMech[j];
        buf[m++] = uChem[j];
      }
    } else {
      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
      dvz = pbc[2]*h_rate[2];
      for (i = 0; i < n; i++) {
        j = list[i];
        buf[m++] = x[j][0] + dx;
        buf[m++] = x[j][1] + dy;
        buf[m++] = x[j][2] + dz;
        if (mask[i] & deform_groupbit) {
          buf[m++] = v[j][0] + dvx;
          buf[m++] = v[j][1] + dvy;
          buf[m++] = v[j][2] + dvz;
        } else {
          buf[m++] = v[j][0];
          buf[m++] = v[j][1];
          buf[m++] = v[j][2];
        }
        buf[m++] = dpdTheta[j];
        buf[m++] = uCond[j];
        buf[m++] = uMech[j];
        buf[m++] = uChem[j];
      }
    }
  }
  return m;
}

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

void AtomVecDPD::unpack_comm(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    x[i][0] = buf[m++];
    x[i][1] = buf[m++];
    x[i][2] = buf[m++];
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
  }
}

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

void AtomVecDPD::unpack_comm_vel(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    x[i][0] = buf[m++];
    x[i][1] = buf[m++];
    x[i][2] = buf[m++];
    v[i][0] = buf[m++];
    v[i][1] = buf[m++];
    v[i][2] = buf[m++];
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
  }
}

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

int AtomVecDPD::pack_reverse(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    buf[m++] = f[i][0];
    buf[m++] = f[i][1];
    buf[m++] = f[i][2];
  }
  return m;
}

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

void AtomVecDPD::unpack_reverse(int n, int *list, double *buf)
{
  int i,j,m;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    f[j][0] += buf[m++];
    f[j][1] += buf[m++];
    f[j][2] += buf[m++];
  }
}

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

int AtomVecDPD::pack_border(int n, int *list, double *buf,
                               int pbc_flag, int *pbc)
{
  int i,j,m;
  double dx,dy,dz;

  m = 0;
  if (pbc_flag == 0) {
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0];
      buf[m++] = x[j][1];
      buf[m++] = x[j][2];
      buf[m++] = ubuf(tag[j]).d;
      buf[m++] = ubuf(type[j]).d;
      buf[m++] = ubuf(mask[j]).d;
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
      buf[m++] = uCG[j];
      buf[m++] = uCGnew[j];
    }
  } else {
    if (domain->triclinic == 0) {
      dx = pbc[0]*domain->xprd;
      dy = pbc[1]*domain->yprd;
      dz = pbc[2]*domain->zprd;
    } else {
      dx = pbc[0];
      dy = pbc[1];
      dz = pbc[2];
    }
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0] + dx;
      buf[m++] = x[j][1] + dy;
      buf[m++] = x[j][2] + dz;
      buf[m++] = ubuf(tag[j]).d;
      buf[m++] = ubuf(type[j]).d;
      buf[m++] = ubuf(mask[j]).d;
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
      buf[m++] = uCG[j];
      buf[m++] = uCGnew[j];
    }
  }

  if (atom->nextra_border)
    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);

  return m;
}

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

int AtomVecDPD::pack_border_vel(int n, int *list, double *buf,
                                   int pbc_flag, int *pbc)
{
  int i,j,m;
  double dx,dy,dz,dvx,dvy,dvz;

  m = 0;
  if (pbc_flag == 0) {
    for (i = 0; i < n; i++) {
      j = list[i];
      buf[m++] = x[j][0];
      buf[m++] = x[j][1];
      buf[m++] = x[j][2];
      buf[m++] = ubuf(tag[j]).d;
      buf[m++] = ubuf(type[j]).d;
      buf[m++] = ubuf(mask[j]).d;
      buf[m++] = v[j][0];
      buf[m++] = v[j][1];
      buf[m++] = v[j][2];
      buf[m++] = dpdTheta[j];
      buf[m++] = uCond[j];
      buf[m++] = uMech[j];
      buf[m++] = uChem[j];
      buf[m++] = uCG[j];
      buf[m++] = uCGnew[j];
    }
  } else {
    if (domain->triclinic == 0) {
      dx = pbc[0]*domain->xprd;
      dy = pbc[1]*domain->yprd;
      dz = pbc[2]*domain->zprd;
    } else {
      dx = pbc[0];
      dy = pbc[1];
      dz = pbc[2];
    }
    if (!deform_vremap) {
      for (i = 0; i < n; i++) {
        j = list[i];
        buf[m++] = x[j][0] + dx;
        buf[m++] = x[j][1] + dy;
        buf[m++] = x[j][2] + dz;
        buf[m++] = ubuf(tag[j]).d;
        buf[m++] = ubuf(type[j]).d;
        buf[m++] = ubuf(mask[j]).d;
        buf[m++] = v[j][0];
        buf[m++] = v[j][1];
        buf[m++] = v[j][2];
        buf[m++] = dpdTheta[j];
        buf[m++] = uCond[j];
        buf[m++] = uMech[j];
        buf[m++] = uChem[j];
        buf[m++] = uCG[j];
        buf[m++] = uCGnew[j];
      }
    } else {
      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
      dvz = pbc[2]*h_rate[2];
      for (i = 0; i < n; i++) {
        j = list[i];
        buf[m++] = x[j][0] + dx;
        buf[m++] = x[j][1] + dy;
        buf[m++] = x[j][2] + dz;
        buf[m++] = ubuf(tag[j]).d;
        buf[m++] = ubuf(type[j]).d;
        buf[m++] = ubuf(mask[j]).d;
        if (mask[i] & deform_groupbit) {
          buf[m++] = v[j][0] + dvx;
          buf[m++] = v[j][1] + dvy;
          buf[m++] = v[j][2] + dvz;
        } else {
          buf[m++] = v[j][0];
          buf[m++] = v[j][1];
          buf[m++] = v[j][2];
        }
        buf[m++] = dpdTheta[j];
        buf[m++] = uCond[j];
        buf[m++] = uMech[j];
        buf[m++] = uChem[j];
        buf[m++] = uCG[j];
        buf[m++] = uCGnew[j];
      }
    }
  }

  if (atom->nextra_border)
    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);

  return m;
}

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

int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf)
{
  int i,j,m;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    buf[m++] = dpdTheta[j];
    buf[m++] = uCond[j];
    buf[m++] = uMech[j];
    buf[m++] = uChem[j];
  }
  return m;
}

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

int AtomVecDPD::pack_border_hybrid(int n, int *list, double *buf)
{
  int i,j,m;

  m = 0;
  for (i = 0; i < n; i++) {
    j = list[i];
    buf[m++] = dpdTheta[j];
    buf[m++] = uCond[j];
    buf[m++] = uMech[j];
    buf[m++] = uChem[j];
    buf[m++] = uCG[j];
    buf[m++] = uCGnew[j];
  }
  return m;
}

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

void AtomVecDPD::unpack_border(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    if (i == nmax) grow(0);
    x[i][0] = buf[m++];
    x[i][1] = buf[m++];
    x[i][2] = buf[m++];
    tag[i] = (tagint) ubuf(buf[m++]).i;
    type[i] = (int) ubuf(buf[m++]).i;
    mask[i] = (int) ubuf(buf[m++]).i;
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
    uCG[i] = buf[m++];
    uCGnew[i] = buf[m++];
  }

  if (atom->nextra_border)
    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
      m += modify->fix[atom->extra_border[iextra]]->
        unpack_border(n,first,&buf[m]);
}

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

void AtomVecDPD::unpack_border_vel(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    if (i == nmax) grow(0);
    x[i][0] = buf[m++];
    x[i][1] = buf[m++];
    x[i][2] = buf[m++];
    tag[i] = (tagint) ubuf(buf[m++]).i;
    type[i] = (int) ubuf(buf[m++]).i;
    mask[i] = (int) ubuf(buf[m++]).i;
    v[i][0] = buf[m++];
    v[i][1] = buf[m++];
    v[i][2] = buf[m++];
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
    uCG[i] = buf[m++];
    uCGnew[i] = buf[m++];
  }

  if (atom->nextra_border)
    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
      m += modify->fix[atom->extra_border[iextra]]->
        unpack_border(n,first,&buf[m]);
}

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

int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
  }
  return m;
}

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

int AtomVecDPD::unpack_border_hybrid(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++) {
    dpdTheta[i] = buf[m++];
    uCond[i] = buf[m++];
    uMech[i] = buf[m++];
    uChem[i] = buf[m++];
    uCG[i] = buf[m++];
    uCGnew[i] = buf[m++];
  }
  return m;
}

/* ----------------------------------------------------------------------
   pack data for atom I for sending to another proc
   xyz must be 1st 3 values, so comm::exchange() can test on them
------------------------------------------------------------------------- */

int AtomVecDPD::pack_exchange(int i, double *buf)
{
  int m = 1;
  buf[m++] = x[i][0];
  buf[m++] = x[i][1];
  buf[m++] = x[i][2];
  buf[m++] = v[i][0];
  buf[m++] = v[i][1];
  buf[m++] = v[i][2];
  buf[m++] = ubuf(tag[i]).d;
  buf[m++] = ubuf(type[i]).d;
  buf[m++] = ubuf(mask[i]).d;
  buf[m++] = ubuf(image[i]).d;
  buf[m++] = dpdTheta[i];
  buf[m++] = uCond[i];
  buf[m++] = uMech[i];
  buf[m++] = uChem[i];
  buf[m++] = uCG[i];
  buf[m++] = uCGnew[i];

  if (atom->nextra_grow)
    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);

  buf[0] = m;
  return m;
}

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

int AtomVecDPD::unpack_exchange(double *buf)
{
  int nlocal = atom->nlocal;
  if (nlocal == nmax) grow(0);

  int m = 1;
  x[nlocal][0] = buf[m++];
  x[nlocal][1] = buf[m++];
  x[nlocal][2] = buf[m++];
  v[nlocal][0] = buf[m++];
  v[nlocal][1] = buf[m++];
  v[nlocal][2] = buf[m++];
  tag[nlocal] = (tagint) ubuf(buf[m++]).i;
  type[nlocal] = (int) ubuf(buf[m++]).i;
  mask[nlocal] = (int) ubuf(buf[m++]).i;
  image[nlocal] = (imageint) ubuf(buf[m++]).i;
  dpdTheta[nlocal] = buf[m++];
  uCond[nlocal] = buf[m++];
  uMech[nlocal] = buf[m++];
  uChem[nlocal] = buf[m++];
  uCG[nlocal] = buf[m++];
  uCGnew[nlocal] = buf[m++];

  if (atom->nextra_grow)
    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
      m += modify->fix[atom->extra_grow[iextra]]->
        unpack_exchange(nlocal,&buf[m]);

  atom->nlocal++;
  return m;
}

/* ----------------------------------------------------------------------
   size of restart data for all atoms owned by this proc
   include extra data stored by fixes
------------------------------------------------------------------------- */

int AtomVecDPD::size_restart()
{
  int i;

  int nlocal = atom->nlocal;
  int n = 15 * nlocal; // 11 + dpdTheta + uCond + uMech + uChem

  if (atom->nextra_restart)
    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
      for (i = 0; i < nlocal; i++)
        n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);

  return n;
}

/* ----------------------------------------------------------------------
   pack atom I's data for restart file including extra quantities
   xyz must be 1st 3 values, so that read_restart can test on them
   molecular types may be negative, but write as positive
------------------------------------------------------------------------- */

int AtomVecDPD::pack_restart(int i, double *buf)
{
  int m = 1;
  buf[m++] = x[i][0];
  buf[m++] = x[i][1];
  buf[m++] = x[i][2];
  buf[m++] = ubuf(tag[i]).d;
  buf[m++] = ubuf(type[i]).d;
  buf[m++] = ubuf(mask[i]).d;
  buf[m++] = ubuf(image[i]).d;
  buf[m++] = v[i][0];
  buf[m++] = v[i][1];
  buf[m++] = v[i][2];
  buf[m++] = dpdTheta[i];
  buf[m++] = uCond[i];
  buf[m++] = uMech[i];
  buf[m++] = uChem[i];

  if (atom->nextra_restart)
    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);

  buf[0] = m;
  return m;
}

/* ----------------------------------------------------------------------
   unpack data for one atom from restart file including extra quantities
------------------------------------------------------------------------- */

int AtomVecDPD::unpack_restart(double *buf)
{
  int nlocal = atom->nlocal;
  if (nlocal == nmax) {
    grow(0);
    if (atom->nextra_store)
      memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
  }

  int m = 1;
  x[nlocal][0] = buf[m++];
  x[nlocal][1] = buf[m++];
  x[nlocal][2] = buf[m++];
  tag[nlocal] = (tagint) ubuf(buf[m++]).i;
  type[nlocal] = (int) ubuf(buf[m++]).i;
  mask[nlocal] = (int) ubuf(buf[m++]).i;
  image[nlocal] = (imageint) ubuf(buf[m++]).i;
  v[nlocal][0] = buf[m++];
  v[nlocal][1] = buf[m++];
  v[nlocal][2] = buf[m++];
  dpdTheta[nlocal] = buf[m++];
  uCond[nlocal] = buf[m++];
  uMech[nlocal] = buf[m++];
  uChem[nlocal] = buf[m++];

  double **extra = atom->extra;
  if (atom->nextra_store) {
    int size = static_cast<int> (buf[0]) - m;
    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
  }

  atom->nlocal++;
  return m;
}

/* ----------------------------------------------------------------------
   create one atom of itype at coord
   set other values to defaults
------------------------------------------------------------------------- */

void AtomVecDPD::create_atom(int itype, double *coord)
{
  int nlocal = atom->nlocal;
  if (nlocal == nmax) grow(0);

  tag[nlocal] = 0;
  type[nlocal] = itype;
  x[nlocal][0] = coord[0];
  x[nlocal][1] = coord[1];
  x[nlocal][2] = coord[2];
  mask[nlocal] = 1;
  image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
    ((imageint) IMGMAX << IMGBITS) | IMGMAX;
  v[nlocal][0] = 0.0;
  v[nlocal][1] = 0.0;
  v[nlocal][2] = 0.0;
  rho[nlocal] = 0.0;
  dpdTheta[nlocal] = 0.0;
  uCond[nlocal] = 0.0;
  uMech[nlocal] = 0.0;
  uChem[nlocal] = 0.0;
  uCG[nlocal] = 0.0;
  uCGnew[nlocal] = 0.0;
  duChem[nlocal] = 0.0;

  atom->nlocal++;
}

/* ----------------------------------------------------------------------
   unpack one line from Atoms section of data file
   initialize other atom quantities
------------------------------------------------------------------------- */

void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values)
{
  int nlocal = atom->nlocal;
  if (nlocal == nmax) grow(0);

  tag[nlocal] = ATOTAGINT(values[0]);
  type[nlocal] = atoi(values[1]);
  if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
    error->one(FLERR,"Invalid atom type in Atoms section of data file");

  dpdTheta[nlocal] = atof(values[2]);
  if (dpdTheta[nlocal] <= 0)
    error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero");

  x[nlocal][0] = coord[0];
  x[nlocal][1] = coord[1];
  x[nlocal][2] = coord[2];

  image[nlocal] = imagetmp;

  mask[nlocal] = 1;
  v[nlocal][0] = 0.0;
  v[nlocal][1] = 0.0;
  v[nlocal][2] = 0.0;

  rho[nlocal] = 0.0;
  uCond[nlocal] = 0.0;
  uMech[nlocal] = 0.0;
  uChem[nlocal] = 0.0;
  uCG[nlocal] = 0.0;
  uCGnew[nlocal] = 0.0;

  atom->nlocal++;
}

/* ----------------------------------------------------------------------
   unpack hybrid quantities from one line in Atoms section of data file
   initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */

int AtomVecDPD::data_atom_hybrid(int nlocal, char **values)
{
  dpdTheta[nlocal] = atof(values[0]);

  return 1;
}

/* ----------------------------------------------------------------------
   pack atom info for data file including 3 image flags
------------------------------------------------------------------------- */

void AtomVecDPD::pack_data(double **buf)
{
  int nlocal = atom->nlocal;
  for (int i = 0; i < nlocal; i++) {
    buf[i][0] = ubuf(tag[i]).d;
    buf[i][1] = ubuf(type[i]).d;
    buf[i][2] = dpdTheta[i];
    buf[i][3] = x[i][0];
    buf[i][4] = x[i][1];
    buf[i][5] = x[i][2];
    buf[i][6] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
    buf[i][7] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
    buf[i][8] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
  }
}

/* ----------------------------------------------------------------------
   pack hybrid atom info for data file
------------------------------------------------------------------------- */

int AtomVecDPD::pack_data_hybrid(int i, double *buf)
{
  buf[0] = dpdTheta[i];
  return 1;
}

/* ----------------------------------------------------------------------
   write atom info to data file including 3 image flags
------------------------------------------------------------------------- */

void AtomVecDPD::write_data(FILE *fp, int n, double **buf)
{
  for (int i = 0; i < n; i++)
    fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
            (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
            buf[i][2],buf[i][3],buf[i][4],buf[i][5],
            (int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i,
            (int) ubuf(buf[i][8]).i);
}

/* ----------------------------------------------------------------------
   write hybrid atom info to data file
------------------------------------------------------------------------- */

int AtomVecDPD::write_data_hybrid(FILE *fp, double *buf)
{
  fprintf(fp," %-1.16e",buf[0]);
  return 1;
}

/* ----------------------------------------------------------------------
   return # of bytes of allocated memory
------------------------------------------------------------------------- */

bigint AtomVecDPD::memory_usage()
{
  bigint bytes = 0;

  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
  if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
  if (atom->memcheck("rho")) bytes += memory->usage(rho,nmax);
  if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax);
  if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax);
  if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax);
  if (atom->memcheck("uChem")) bytes += memory->usage(uChem,nmax);
  if (atom->memcheck("uCG")) bytes += memory->usage(uCG,nmax);
  if (atom->memcheck("uCGnew")) bytes += memory->usage(uCGnew,nmax);
  if (atom->memcheck("duChem")) bytes += memory->usage(duChem,nmax);

  return bytes;
}
