/* ----------------------------------------------------------------------
   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: G. Ziegenhain, gerolf@ziegenhain.com
                        Copyright (C) 2007
------------------------------------------------------------------------- */

#include "string.h"
#include "compute_ackland_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <math.h>

using namespace LAMMPS_NS;

enum{UNKNOWN,BCC,FCC,HCP,ICO};

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

ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
  Compute(lmp, narg, arg)
{
  if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command");

  peratom_flag = 1;
  size_peratom_cols = 0;

  nmax = 0;
  structure = NULL;
  maxneigh = 0;
  distsq = NULL;
  nearest = NULL;
  nearest_n0 = NULL;
  nearest_n1 = NULL;
}

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

ComputeAcklandAtom::~ComputeAcklandAtom()
{
  memory->destroy(structure);
  memory->destroy(distsq);
  memory->destroy(nearest);
  memory->destroy(nearest_n0);
  memory->destroy(nearest_n1);
}

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

void ComputeAcklandAtom::init()
{
  // need an occasional full neighbor list

  int irequest = neighbor->request((void *) this);
  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;

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

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

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

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

void ComputeAcklandAtom::compute_peratom()
{
  int i,j,ii,jj,k,n,inum,jnum;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *ilist,*jlist,*numneigh,**firstneigh;
  int chi[8];

  invoked_peratom = update->ntimestep;

  // grow structure array if necessary

  if (atom->nlocal > nmax) {
    memory->destroy(structure);
    nmax = atom->nmax;
    memory->create(structure,nmax,"compute/ackland/atom:ackland");
    vector_atom = structure;
  }

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

  neighbor->build_one(list->index);

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

  // compute structure parameter for each atom in group
  // use full neighbor list

  double **x = atom->x;
  int *mask = atom->mask;
  double cutsq = force->pair->cutforce * force->pair->cutforce;

  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];

      // ensure distsq and nearest arrays are long enough

      if (jnum > maxneigh) {
      	memory->destroy(distsq);
      	memory->destroy(nearest);
	memory->destroy(nearest_n0);
	memory->destroy(nearest_n1);
      	maxneigh = jnum;
      	memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
      	memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
	memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
	memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
      }

      // loop over list of all neighbors within force cutoff
      // distsq[] = distance sq to each
      // nearest[] = atom indices of neighbors

      n = 0;
      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;
      	if (rsq < cutsq) {
	  distsq[n] = rsq;
	  nearest[n++] = j;
	}  
      }

      // Select 6 nearest neighbors

      select2(6,n,distsq,nearest);

      // Mean squared separation

      double r0_sq = 0.;
      for (j = 0; j < 6; j++) 
	r0_sq += distsq[j];
      r0_sq /= 6.;

      // n0 near neighbors with: distsq<1.45*r0_sq
      // n1 near neighbors with: distsq<1.55*r0_sq

      double n0_dist_sq = 1.45*r0_sq,
	n1_dist_sq = 1.55*r0_sq;
      int n0 = 0, n1 = 0;
      for (j = 0; j < n; j++) {
         if (distsq[j] < n1_dist_sq) {
            nearest_n1[n1++] = nearest[j];
            if (distsq[j] < n0_dist_sq) {
               nearest_n0[n0++] = nearest[j];
            }
         }
      }

      // Evaluate all angles <(r_ij,rik) forall n0 particles with:
      // distsq < 1.45*r0_sq

      double bond_angle;
      double norm_j, norm_k;
      chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
      double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik;
      for (j = 0; j < n0; j++) {
	x_ij = x[i][0]-x[nearest_n0[j]][0];
	y_ij = x[i][1]-x[nearest_n0[j]][1];
	z_ij = x[i][2]-x[nearest_n0[j]][2];
	norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
	if (norm_j <= 0.) continue;
	for (k = j+1; k < n0; k++) {
	  x_ik = x[i][0]-x[nearest_n0[k]][0];
	  y_ik = x[i][1]-x[nearest_n0[k]][1];
	  z_ik = x[i][2]-x[nearest_n0[k]][2];
	  norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
	  if (norm_k <= 0.)
	    continue;

	  bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
	  
	  // Histogram for identifying the relevant peaks

	  if (bond_angle < -0.945) chi[0]++;
	  else if (bond_angle < -0.915) chi[1]++;
	  else if (bond_angle < -0.755) chi[2]++;
	  else if (bond_angle < -0.195) chi[3]++;
	  else if (bond_angle < 0.195) chi[4]++;
	  else if (bond_angle < 0.245) chi[5]++;
	  else if (bond_angle < 0.795) chi[6]++;
	  else chi[7]++;
	}
      }

      // Deviations from the different lattice structures

      double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
      double delta_cp = fabs(1.-(double)chi[6]/24.);
      double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
			       (double)chi[2])/6.0;
      double delta_hcp = (fabs((double)chi[0]-3.)+
			  fabs((double)chi[0]+(double)chi[1]+
			       (double)chi[2]+(double)chi[3]-9.0))/12.0;
      
      // Identification of the local structure according to the reference

      if (chi[0] == 7)       { delta_bcc = 0.; }
      else if (chi[0] == 6)  { delta_fcc = 0.; }
      else if (chi[0] <= 3)  { delta_hcp = 0.; }

      if (chi[7] > 0.)  
         structure[i] = UNKNOWN; 
      else 
      if (chi[4] < 3.) 
      {
         if (n1 > 13 || n1 < 11) 
            structure[i] = UNKNOWN; 
         else 
            structure[i] = ICO; 
      } else 
      if (delta_bcc <= delta_cp) 
      {
         if (n1 < 11) 
            structure[i] = UNKNOWN; 
         else 
            structure[i] = BCC; 
      } else 
      if (n1 > 12 || n1 < 11) 
         structure[i] = UNKNOWN; 
      else 
      if (delta_fcc < delta_hcp) 
         structure[i] = FCC; 
      else 
         structure[i] = HCP; 

    } else structure[i] = 0.0;
  }
}

/* ----------------------------------------------------------------------
   2 select routines from Numerical Recipes (slightly modified)
   find k smallest values in array of length n
   2nd routine sorts auxiliary array at same time
------------------------------------------------------------------------- */

#define SWAP(a,b)   tmp = a; a = b; b = tmp;
#define ISWAP(a,b) itmp = a; a = b; b = itmp;

void ComputeAcklandAtom::select(int k, int n, double *arr)
  {
  int i,ir,j,l,mid;
  double a,tmp;

  arr--;
  l = 1;
  ir = n;
  for (;;) {
    if (ir <= l+1) {
      if (ir == l+1 && arr[ir] < arr[l]) {
	SWAP(arr[l],arr[ir])
      }
      return;
    } else {
      mid=(l+ir) >> 1;
      SWAP(arr[mid],arr[l+1])
      if (arr[l] > arr[ir]) {
	SWAP(arr[l],arr[ir])
      }
      if (arr[l+1] > arr[ir]) {
	SWAP(arr[l+1],arr[ir])
      }
      if (arr[l] > arr[l+1]) {
	SWAP(arr[l],arr[l+1])
      }
      i = l+1;
      j = ir;
      a = arr[l+1];
      for (;;) {
	do i++; while (arr[i] < a);
	do j--; while (arr[j] > a);
	if (j < i) break;
	SWAP(arr[i],arr[j])
      }
      arr[l+1] = arr[j];
      arr[j] = a;
      if (j >= k) ir = j-1;
      if (j <= k) l = i;
    }
  }
}

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

void ComputeAcklandAtom::select2(int k, int n, double *arr, int *iarr)
{
  int i,ir,j,l,mid,ia,itmp;
  double a,tmp;

  arr--;
  iarr--;
  l = 1;
  ir = n;
  for (;;) {
    if (ir <= l+1) {
      if (ir == l+1 && arr[ir] < arr[l]) {
	SWAP(arr[l],arr[ir])
	ISWAP(iarr[l],iarr[ir])
      }
      return;
    } else {
      mid=(l+ir) >> 1;
      SWAP(arr[mid],arr[l+1])
      ISWAP(iarr[mid],iarr[l+1])
      if (arr[l] > arr[ir]) {
	SWAP(arr[l],arr[ir])
	ISWAP(iarr[l],iarr[ir])
      }
      if (arr[l+1] > arr[ir]) {
	SWAP(arr[l+1],arr[ir])
	ISWAP(iarr[l+1],iarr[ir])
      }
      if (arr[l] > arr[l+1]) {
	SWAP(arr[l],arr[l+1])
	ISWAP(iarr[l],iarr[l+1])
      }
      i = l+1;
      j = ir;
      a = arr[l+1];
      ia = iarr[l+1];
      for (;;) {
	do i++; while (arr[i] < a);
	do j--; while (arr[j] > a);
	if (j < i) break;
	SWAP(arr[i],arr[j])
	ISWAP(iarr[i],iarr[j])
      }
      arr[l+1] = arr[j];
      arr[j] = a;
      iarr[l+1] = iarr[j];
      iarr[j] = ia;
      if (j >= k) ir = j-1;
      if (j <= k) l = i;
    }
  }
}

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

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