/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#include "compute_collision_contact.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <algorithm>
#include "group.h"

using namespace LAMMPS_NS;

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

ComputeCollisionContact::ComputeCollisionContact(LAMMPS *lmp, int narg, char **arg) :
  Compute(lmp, narg, arg),
  contact(NULL), contactall(NULL), contactPerAtom(NULL), radiuses(NULL), atomChunkID(NULL),
  neighbourChunk(NULL)
{
  if (narg < 5) error->all(FLERR,"Illegal compute collision/contact command");
  if (narg - 5 != atom->ntypes * 2) error->all(FLERR,"Illegal compute collision/contact command. "
                                               "Number of types does not match the given radiuses");

  memory->create(radiuses,atom->ntypes,"collision/contact:radiuses");

  startstep = 0;

  int iarg = 3;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"start") == 0) {
      startstep = force->inumeric(FLERR,arg[iarg+1]);
      startstep--;    
      iarg += 2;
    } else {
      radiuses[force->inumeric(FLERR,arg[iarg])-1] = force->numeric(FLERR,arg[iarg+1]);
      iarg += 2;
    }
  }

  if (startstep == 0) 
    error->all(FLERR,"Start time must be specified for collision/contact compute");

  peratom_flag = 1;
  size_peratom_cols = 0;
  comm_reverse = 1;

  nmax = 0;
  nmol = 0;

  MPI_Comm_size(world,&nprocs);

}

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

ComputeCollisionContact::~ComputeCollisionContact()
{
  memory->destroy(contact);
  memory->destroy(contactall);
  memory->destroy(contactPerAtom);
  memory->destroy(radiuses);
  memory->destroy(atomChunkID);
  memory->destroy(neighbourChunk);
}

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

void ComputeCollisionContact::init()
{
  if (force->pair == NULL)
    error->all(FLERR,"Compute coord/atom requires a pair style be defined");

  int count = 0;
  for (int i = 0; i < modify->ncompute; i++)
    if (strcmp(modify->compute[i]->style,"collision/contact") == 0) count++;
  if (count > 1 && comm->me == 0)
    error->warning(FLERR,"More than one compute collision/contact");

  int ifix = modify->find_fix_by_style("reax/c/species");
  if (ifix < 0)
    error->all(FLERR,"reax/c/species fix does not exist for "
               "compute collision/contact");

  // need an occasional neighbor list

  int irequest = neighbor->request(this,instance_me);
  neighbor->requests[irequest]->pair = 0;
  neighbor->requests[irequest]->compute = 1;
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;
  neighbor->requests[irequest]->occasional = 1;
}

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

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

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

void ComputeCollisionContact::compute_peratom()
{
  int i,j,ii,jj,inum,jnum;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  double radi,radisq;
  int *ilist,*jlist,*numneigh,**firstneigh;

  invoked_peratom = update->ntimestep;

  if (atom->nmax > nmax) {
    memory->destroy(contactPerAtom);
    nmax = atom->nmax;
    memory->create(contactPerAtom,nmax,"c/c:contactPerAtom");
    vector_atom = contactPerAtom;
    memory->create(atomChunkID,nmax,"c/c:atomChunkID");
  }

  for (i = 0; i < nmax; i++) contactPerAtom[i] = 0.0;

  // avoid memory fault due to uninitialized reax/c/species class

  if (update->ntimestep > startstep) {

    // invoke neighbor list (will copy or build if necessary)

    neighbor->build_one(list);

    inum = list->inum;
    ilist = list->ilist;
    numneigh = list->numneigh;
    firstneigh = list->firstneigh;

    // create the chunk arrays

    reaxc = NULL;
    reaxc = (PairReaxC *) force->pair_match("^reax/c",0);

    int *spatomID, *spclusterID;
    spclusterID = reaxc->ke_temp_compute->compute_clusterID;
    spatomID = reaxc->ke_temp_compute->compute_atomID;
    nchunk = reaxc->ke_temp_compute->totalMol;

    // obtain current nchunk of each atom

    int natoms = atom->natoms;
    int ntotal = atom->nlocal + atom->nghost;
    for (i = 0; i < ntotal; i++) {
      for (j = 0; j < natoms; j++) {
        if (atom->tag[i] == spatomID[j]) {
          atomChunkID[i] = spclusterID[j];
        }
      }
    }    

    if (nchunk != nmol) {
      nmol = nchunk;
      memory->destroy(neighbourChunk);
      memory->destroy(contact);
      memory->destroy(contactall);
      memory->create(contact,nchunk,"c/c:contact");
      memory->create(contactall,nchunk,"c/c:contactall");
      memory->create(neighbourChunk,nchunk,nchunk,"c/c:neighbourChunk");
    }

    // neighbourChunk stores 1/0 for each chunk of atom i if a collision was/wasn't counted for 
    // the chunk of atom j

    for (i = 0; i < nchunk; i++) {
      for (j = 0; j < nchunk; j++) {
        neighbourChunk[i][j] = 0;
      }
    } 

    // compute number of contacts for each atom in group
    // collision if distance <= sum of radii
    // tally for both I and J
    // i,j local indeces

    double **x = atom->x;
    int *mask = atom->mask;
    int chunksumIDnow;

    for (i = 0; i < nchunk; i++) contact[i] = 0.0;

    for (ii = 0; ii < inum; ii++) {
      i = ilist[ii];
      if (mask[i] & groupbit) {
        xtmp = x[i][0];
        ytmp = x[i][1];
        ztmp = x[i][2];
        jlist = firstneigh[i];
        jnum = numneigh[i];

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

          if (atomChunkID[i] != atomChunkID[j]) {                             // if atom j does not belong in the same molecule as i
            if (neighbourChunk[atomChunkID[i]-1][atomChunkID[j]-1] == 0) {    // check if collision with neighbour chunk has been already counted

              radi = radiuses[atom->type[i]-1]+radiuses[atom->type[j]-1];
              radisq = radi*radi;
 
              delx = xtmp - x[j][0];
              dely = ytmp - x[j][1];
              delz = ztmp - x[j][2];
              rsq = delx*delx + dely*dely + delz*delz;

              if (rsq <= radisq) {
                contact[atomChunkID[i]-1] += 1.0;
                neighbourChunk[atomChunkID[i]-1][atomChunkID[j]-1] = 1;
              }
            }
          }
        }
      }
    }

    // in case a molecule is located between two processors communicate the information of collisions
    // between all processors. Therefore, this will count all collisions even if half the molecule is 
    // in ghost atoms for that processor
    MPI_Allreduce(contact,contactall,nchunk,MPI_DOUBLE,MPI_SUM,world);

    // chunk values to atoms
    for (i = 0; i < inum; i++) {
      contactPerAtom[i] = contactall[atomChunkID[i]-1];
    }
  }

  // communicate ghost atom counts between neighbor procs if necessary

  if (force->newton_pair) comm->reverse_comm_compute(this);
}

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

int ComputeCollisionContact::pack_reverse_comm(int n, int first, double *buf)
{
  int i,m,last;

  m = 0;
  last = first + n;
  for (i = first; i < last; i++)
    buf[m++] = contactPerAtom[i];
  return m;
}

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

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

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

/* ----------------------------------------------------------------------
   memory usage of local atom-based array
------------------------------------------------------------------------- */

double ComputeCollisionContact::memory_usage()
{
  double bytes = nmax * sizeof(double);
  return bytes;
}