/* ----------------------------------------------------------------------
   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 <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_body.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "body_nparticle.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#define DELTA 10000

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

PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
{
  dmax = nmax = 0;
  discrete = NULL;
  dnum = dfirst = NULL;

  single_enable = 0;
  restartinfo = 0;
}

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

PairBody::~PairBody()
{
  memory->destroy(discrete);
  memory->destroy(dnum);
  memory->destroy(dfirst);

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(epsilon);
    memory->destroy(sigma);
    memory->destroy(lj1);
    memory->destroy(lj2);
    memory->destroy(lj3);
    memory->destroy(lj4);
  }
}

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

void PairBody::compute(int eflag, int vflag)
{
  int i,j,ii,jj,inum,jnum,itype,jtype;
  int ni,nj,npi,npj,ifirst,jfirst;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double rsq,r2inv,r6inv,forcelj;
  double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3];
  double *dxi,*dxj;
  int *ilist,*jlist,*numneigh,**firstneigh;

  evdwl = 0.0;
  if (eflag || vflag) ev_setup(eflag,vflag);
  else evflag = vflag_fdotr = 0;

  double **x = atom->x;
  double **f = atom->f;
  double **torque = atom->torque;
  int *body = atom->body;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  int newton_pair = force->newton_pair;

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

  // grow discrete list if necessary and initialize

  if (nall > nmax) {
    nmax = nall;
    memory->destroy(dnum);
    memory->destroy(dfirst);
    memory->create(dnum,nall,"pair:dnum");
    memory->create(dfirst,nall,"pair:dfirst");
  }
  for (i = 0; i < nall; i++) dnum[i] = 0;
  ndiscrete = 0;

  // loop over neighbors of my atoms

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

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

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

      if (rsq >= cutsq[itype][jtype]) continue;

      // body/body interactions = NxM sub-particles

      evdwl = 0.0;
      if (body[i] >= 0 && body[j] >= 0) {
        if (dnum[i] == 0) body2space(i);
        npi = dnum[i];
        ifirst = dfirst[i];
        if (dnum[j] == 0) body2space(j);
        npj = dnum[j];
        jfirst = dfirst[j];

        for (ni = 0; ni < npi; ni++) {
          dxi = discrete[ifirst+ni];

          for (nj = 0; nj < npj; nj++) {
            dxj = discrete[jfirst+nj];

            xi[0] = x[i][0] + dxi[0];
            xi[1] = x[i][1] + dxi[1];
            xi[2] = x[i][2] + dxi[2];
            xj[0] = x[j][0] + dxj[0];
            xj[1] = x[j][1] + dxj[1];
            xj[2] = x[j][2] + dxj[2];

            delx = xi[0] - xj[0];
            dely = xi[1] - xj[1];
            delz = xi[2] - xj[2];
            rsq = delx*delx + dely*dely + delz*delz;

            r2inv = 1.0/rsq;
            r6inv = r2inv*r2inv*r2inv;
            forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
            fpair = forcelj*r2inv;

            if (eflag)
              evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);

            fi[0] = delx*fpair;
            fi[1] = dely*fpair;
            fi[2] = delz*fpair;
            f[i][0] += fi[0];
            f[i][1] += fi[1];
            f[i][2] += fi[2];
            ti[0] = dxi[1]*fi[2] - dxi[2]*fi[1];
            ti[1] = dxi[2]*fi[0] - dxi[0]*fi[2];
            ti[2] = dxi[0]*fi[1] - dxi[1]*fi[0];
            torque[i][0] += ti[0];
            torque[i][1] += ti[1];
            torque[i][2] += ti[2];

            if (newton_pair || j < nlocal) {
              fj[0] = -delx*fpair;
              fj[1] = -dely*fpair;
              fj[2] = -delz*fpair;
              f[j][0] += fj[0];
              f[j][1] += fj[1];
              f[j][2] += fj[2];
              tj[0] = dxj[1]*fj[2] - dxj[2]*fj[1];
              tj[1] = dxj[2]*fj[0] - dxj[0]*fj[2];
              tj[2] = dxj[0]*fj[1] - dxj[1]*fj[0];
              torque[j][0] += tj[0];
              torque[j][1] += tj[1];
              torque[j][2] += tj[2];
            }
          }
        }

      // body/particle interaction = Nx1 sub-particles

      } else if (body[i] >= 0) {
        if (dnum[i] == 0) body2space(i);
        npi = dnum[i];
        ifirst = dfirst[i];

        for (ni = 0; ni < npi; ni++) {
          dxi = discrete[ifirst+ni];

          xi[0] = x[i][0] + dxi[0];
          xi[1] = x[i][1] + dxi[1];
          xi[2] = x[i][2] + dxi[2];
          xj[0] = x[j][0];
          xj[1] = x[j][1];
          xj[2] = x[j][2];

          delx = xi[0] - xj[0];
          dely = xi[1] - xj[1];
          delz = xi[2] - xj[2];
          rsq = delx*delx + dely*dely + delz*delz;

          r2inv = 1.0/rsq;
          r6inv = r2inv*r2inv*r2inv;
          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
          fpair = forcelj*r2inv;

          if (eflag)
            evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);

          fi[0] = delx*fpair;
          fi[1] = dely*fpair;
          fi[2] = delz*fpair;
          f[i][0] += fi[0];
          f[i][1] += fi[1];
          f[i][2] += fi[2];
          ti[0] = dxi[1]*fi[2] - dxi[2]*fi[1];
          ti[1] = dxi[2]*fi[0] - dxi[0]*fi[2];
          ti[2] = dxi[0]*fi[1] - dxi[1]*fi[0];
          torque[i][0] += ti[0];
          torque[i][1] += ti[1];
          torque[i][2] += ti[2];

          if (newton_pair || j < nlocal) {
            fj[0] = -delx*fpair;
            fj[1] = -dely*fpair;
            fj[2] = -delz*fpair;
            f[j][0] += fj[0];
            f[j][1] += fj[1];
            f[j][2] += fj[2];
          }
        }


      // particle/body interaction = Nx1 sub-particles

      } else if (body[j] >= 0) {
        if (dnum[j] == 0) body2space(j);
        npj = dnum[j];
        jfirst = dfirst[j];

        for (nj = 0; nj < npj; nj++) {
          dxj = discrete[jfirst+nj];

          xi[0] = x[i][0];
          xi[1] = x[i][1];
          xi[2] = x[i][2];
          xj[0] = x[j][0] + dxj[0];
          xj[1] = x[j][1] + dxj[1];
          xj[2] = x[j][2] + dxj[2];

          delx = xi[0] - xj[0];
          dely = xi[1] - xj[1];
          delz = xi[2] - xj[2];
          rsq = delx*delx + dely*dely + delz*delz;

          r2inv = 1.0/rsq;
          r6inv = r2inv*r2inv*r2inv;
          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
          fpair = forcelj*r2inv;

          if (eflag)
            evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);

          fi[0] = delx*fpair;
          fi[1] = dely*fpair;
          fi[2] = delz*fpair;
          f[i][0] += fi[0];
          f[i][1] += fi[1];
          f[i][2] += fi[2];

          if (newton_pair || j < nlocal) {
            fj[0] = -delx*fpair;
            fj[1] = -dely*fpair;
            fj[2] = -delz*fpair;
            f[j][0] += fj[0];
            f[j][1] += fj[1];
            f[j][2] += fj[2];
            tj[0] = dxj[1]*fj[2] - dxj[2]*fj[1];
            tj[1] = dxj[2]*fj[0] - dxj[0]*fj[2];
            tj[2] = dxj[0]*fj[1] - dxj[1]*fj[0];
            torque[j][0] += tj[0];
            torque[j][1] += tj[1];
            torque[j][2] += tj[2];
          }
        }

      // particle/particle interaction = 1x1 particles

      } else {
        r2inv = 1.0/rsq;
        r6inv = r2inv*r2inv*r2inv;
        forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
        fpair = forcelj*r2inv;

        if (eflag)
          evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);

        f[i][0] += delx*fpair;
        f[i][1] += dely*fpair;
        f[i][2] += delz*fpair;
        if (newton_pair || j < nlocal) {
          f[j][0] -= delx*fpair;
          f[j][1] -= dely*fpair;
          f[j][2] -= delz*fpair;
        }
      }

      if (evflag) ev_tally(i,j,nlocal,newton_pair,
                           evdwl,0.0,fpair,delx,dely,delz);
    }
  }

  if (vflag_fdotr) virial_fdotr_compute();
}

/* ----------------------------------------------------------------------
   allocate all arrays
------------------------------------------------------------------------- */

void PairBody::allocate()
{
  allocated = 1;
  int n = atom->ntypes;

  memory->create(setflag,n+1,n+1,"pair:setflag");
  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++)
      setflag[i][j] = 0;

  memory->create(cutsq,n+1,n+1,"pair:cutsq");

  memory->create(cut,n+1,n+1,"pair:cut");
  memory->create(epsilon,n+1,n+1,"pair:epsilon");
  memory->create(sigma,n+1,n+1,"pair:sigma");
  memory->create(lj1,n+1,n+1,"pair:lj1");
  memory->create(lj2,n+1,n+1,"pair:lj2");
  memory->create(lj3,n+1,n+1,"pair:lj3");
  memory->create(lj4,n+1,n+1,"pair:lj4");
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void PairBody::settings(int narg, char **arg)
{
  if (narg != 1) error->all(FLERR,"Illegal pair_style command");

  cut_global = force->numeric(FLERR,arg[0]);

  // reset cutoffs that have been explicitly set

  if (allocated) {
    int i,j;
    for (i = 1; i <= atom->ntypes; i++)
      for (j = i+1; j <= atom->ntypes; j++)
        if (setflag[i][j]) cut[i][j] = cut_global;
  }
}

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairBody::coeff(int narg, char **arg)
{
  if (narg < 4 || narg > 5)
    error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo,ihi,jlo,jhi;
  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);

  double epsilon_one = force->numeric(FLERR,arg[2]);
  double sigma_one = force->numeric(FLERR,arg[3]);

  double cut_one = cut_global;
  if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      epsilon[i][j] = epsilon_one;
      sigma[i][j] = sigma_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
  }

  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairBody::init_style()
{
  avec = (AtomVecBody *) atom->style_match("body");
  if (!avec) error->all(FLERR,"Pair body requires atom style body");
  if (strcmp(avec->bptr->style,"nparticle") != 0)
    error->all(FLERR,"Pair body requires body style nparticle");
  bptr = (BodyNparticle *) avec->bptr;

  neighbor->request(this,instance_me);
}

/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairBody::init_one(int i, int j)
{
  if (setflag[i][j] == 0) {
    epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
                               sigma[i][i],sigma[j][j]);
    sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
  }

  lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
  lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
  lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
  lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);

  epsilon[j][i] = epsilon[i][j];
  sigma[j][i] = sigma[i][j];
  lj1[j][i] = lj1[i][j];
  lj2[j][i] = lj2[i][j];
  lj3[j][i] = lj3[i][j];
  lj4[j][i] = lj4[i][j];

  return cut[i][j];
}

/* ----------------------------------------------------------------------
   convert N sub-particles in body I to space frame using current quaternion
   store sub-particle space-frame displacements from COM in discrete list
------------------------------------------------------------------------- */

void PairBody::body2space(int i)
{
  int ibonus = atom->body[i];
  AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
  int nsub = bptr->nsub(bonus);
  double *coords = bptr->coords(bonus);

  dnum[i] = nsub;
  dfirst[i] = ndiscrete;

  if (ndiscrete + nsub > dmax) {
    dmax += DELTA;
    memory->grow(discrete,dmax,3,"pair:discrete");
  }

  double p[3][3];
  MathExtra::quat_to_mat(bonus->quat,p);

  for (int m = 0; m < nsub; m++) {
    MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]);
    ndiscrete++;
  }
}
