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

   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 authors: Paul Crozier (SNL), Jeff Greathouse (SNL)

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

#include "mpi.h"

#include "math.h"

#include "stdlib.h"

#include "fix_rdf.h"

#include "atom.h"

#include "update.h"

#include "force.h"

#include "domain.h"

#include "output.h"

#include "group.h"

#include "modify.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "neigh_request.h"

#include "pair.h"

#include "force.h"

#include "memory.h"

#include "error.h"

using namespace LAMMPS_NS;

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

FixRDF::FixRDF(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg)

{

  if (narg < 8 || (narg-6) % 2) error->all("Illegal fix rdf command");

  nevery = atoi(arg[3]);

  if (nevery <= 0) error->all("Illegal fix rdf command");

  first = 1;

  MPI_Comm_rank(world,&me);

  if (me == 0) {

    fp = fopen(arg[4],"w");

    if (fp == NULL) {

      char str[128];

      sprintf(str,"Cannot open fix rdf file %s",arg[4]);

      error->one(str);

    }

  }

  maxbin = atoi(arg[5]);

  n_rdf_pairs = 0;

  rdfpair = memory->create_2d_int_array(atom->ntypes+1,atom->ntypes+1,

					"rdf:rdfpair");

  for (int i = 1; i <= atom->ntypes; i++)

    for (int j = 1; j <= atom->ntypes; j++)

      rdfpair[i][j] = 0;

  int itype,jtype;

  for (int i = 6; i < narg; i+=2) {

    itype = atoi(arg[i]);

    jtype = atoi(arg[i+1]);

    if (itype < 1 || jtype < 1 || itype > atom->ntypes || jtype > atom->ntypes)

      error->all("Invalid atom types in fix rdf command");

    n_rdf_pairs++;

    rdfpair[itype][jtype] = n_rdf_pairs;

  }

  hist = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist");

  hist_all = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist_all");

  int *nrdfatom = new int[atom->ntypes+1];

  for (int i = 1; i <= atom->ntypes; i++) nrdfatom[i] = 0;

  int *mask = atom->mask;

  int *type = atom->type;

  int nlocal = atom->nlocal;

  for (int i = 0; i < nlocal; i++)

    if (mask[i] & groupbit) nrdfatom[type[i]]++;

  nrdfatoms = new int[atom->ntypes+1];

  MPI_Allreduce(&nrdfatom[1],&nrdfatoms[1],atom->ntypes,MPI_INT,MPI_SUM,world);

  delete [] nrdfatom;

  gr_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,"rdf:gr_ave");

  ncoord_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,

					      "rdf:nccord_ave");

}

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

FixRDF::~FixRDF()

{

  if (me == 0) fclose(fp);

  memory->destroy_2d_int_array(rdfpair);

  memory->destroy_2d_int_array(hist);

  memory->destroy_2d_int_array(hist_all);

  delete [] nrdfatoms;

  memory->destroy_2d_double_array(gr_ave);

  memory->destroy_2d_double_array(ncoord_ave);

}

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

int FixRDF::setmask()

{

  int mask = 0;

  mask |= END_OF_STEP;

  return mask;

}

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

void FixRDF::init()

{

  if (force->pair) delr = force->pair->cutforce / maxbin;

  else error->all("Fix rdf requires a pair style be defined");

  // need an occasional half neighbor list

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

  neighbor->requests[irequest]->pair = 0;

  neighbor->requests[irequest]->fix = 1;

  neighbor->requests[irequest]->occasional = 1;

  delrinv = 1.0/delr;

  nframes = 0;

  // set running averages to 0.0

  int i,j,bin,irdf;

  for (i = 1; i <= atom->ntypes; i++)

    for (j = 1; j <= atom->ntypes; j++)

      if (rdfpair[i][j]) {

	irdf = rdfpair[i][j] - 1;

	for (bin = 0; bin < maxbin; bin++)

          gr_ave[irdf][bin] = ncoord_ave[irdf][bin] = 0.0;         

      }

}

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

void FixRDF::init_list(int id, NeighList *ptr)

{

  list = ptr;

}

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

void FixRDF::setup(int vflag)

{

  if (first) end_of_step();

  first = 0;

}

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

void FixRDF::end_of_step()

{

  double **x = atom->x;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  int *type = atom->type;

  double *special_coul = force->special_coul;

  double *special_lj = force->special_lj;

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

  int newton_pair = force->newton_pair;

  int i,j,ii,jj,inum,jnum,itype,jtype,ipair,jpair,bin;

  double xtmp,ytmp,ztmp,delx,dely,delz,r;

  int *ilist,*jlist,*numneigh,**firstneigh;

  // invoke half 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;

  // zero the histogram counts

  for (int i = 0; i < n_rdf_pairs; i++)

    for (int j = 0; j < maxbin; j++)

      hist[i][j] = 0;

  // tally the RDF

  // both atom i and j must be in fix group

  // itype,jtype must have been specified by user

  // weighting factor must be != 0.0 for this pair

  //   could be 0 and still be in neigh list for long-range Coulombics

  // count the interaction once even if neighbor pair is stored on 2 procs

  // if itype = jtype, count the interaction twice

  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];

      itype = type[i];

      jlist = firstneigh[i];

      jnum = numneigh[i];

      for (jj = 0; jj < jnum; jj++) {

	j = jlist[jj];

	if (j >= nall) {

	  if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)

	    continue;

	  j %= nall;

	}

        if (mask[j] & groupbit) {

          jtype = type[j];

	  ipair = rdfpair[itype][jtype];

	  jpair = rdfpair[jtype][itype];

	  if (!ipair && !jpair) continue;

          delx = xtmp - x[j][0];

          dely = ytmp - x[j][1];

          delz = ztmp - x[j][2];

          r = sqrt(delx*delx + dely*dely + delz*delz);

          bin = static_cast<int> (r * delrinv);

	  if (bin >= maxbin) continue;

	  if (ipair) hist[ipair-1][bin]++;

	  if (newton_pair || j < nlocal)

	    if (jpair) hist[jpair-1][bin]++;

	}

      }

    }

  }

  // sum histogram across procs

  MPI_Allreduce(hist[0],hist_all[0],n_rdf_pairs*maxbin,MPI_INT,MPI_SUM,world);

  nframes++;

  if (me == 0) {

    // print RDF for current snapshot

    double rlower,rcenter,rupper,nideal,gr;

    double PI = 4.0*atan(1.0);

    double constant = 4.0*PI / (3.0*domain->xprd*domain->yprd*domain->zprd);

    int irdf;

    fprintf(fp,"# Timestep %d\n",update->ntimestep);

    fprintf(fp,"%s","r");

    for (int i = 1; i <= atom->ntypes; i++)

      for (int j = 1; j <= atom->ntypes; j++)

        if (rdfpair[i][j])

          fprintf(fp,", %s%d,%d%s, %s%d,%d%s",

		  "g(",i,j,",r)","ncoord(",i,j,",r)");

    double *ncoord = new double[n_rdf_pairs];   

    for (int i = 0; i < n_rdf_pairs; i++) ncoord[i] = 0;

    for (bin = 0; bin < maxbin; bin++) {

      rlower = bin*delr;

      rcenter = rlower + 0.5*delr;

      rupper = rlower + delr;

      fprintf(fp,"\n%f ",rcenter); 

      for (int i = 1; i <= atom->ntypes; i++)

        for (int j = 1; j <= atom->ntypes; j++)

          if (rdfpair[i][j]) {

            nideal = constant*nrdfatoms[j] *

              (rupper*rupper*rupper - rlower*rlower*rlower);

            irdf = rdfpair[i][j] - 1;

            if (nrdfatoms[i]*nideal != 0.0) 

	      gr = hist_all[irdf][bin] / (nrdfatoms[i]*nideal);

            else gr = 0.0;

            ncoord[irdf] += gr*nideal;

            fprintf(fp,"%f %f ",gr,ncoord[irdf]);  

            gr_ave[irdf][bin] = 

	      ((nframes-1)*gr_ave[irdf][bin] + gr) / nframes;

            ncoord_ave[irdf][bin] = 

	      ((nframes-1)*ncoord_ave[irdf][bin] + ncoord[irdf]) / nframes;

          }

    }

    fprintf(fp,"\n");

    delete [] ncoord;

    // if last time in run that RDF is computed, print running averages

    if (update->ntimestep + nevery > update->endstep) {

      fprintf(fp,"# Run Average\n");

      fprintf(fp,"%s","r");

      for (int i = 1; i <= atom->ntypes; i++)

        for (int j = 1; j <= atom->ntypes; j++)

          if (rdfpair[i][j])

            fprintf(fp,", %s%d,%d%s, %s%d,%d%s",

		    "g(",i,j,",r)","ncoord(",i,j,",r)");

      for (bin = 0; bin < maxbin; bin++) {

        rlower = bin*delr;

        rcenter = rlower + 0.5*delr;

        rupper = rlower + delr;

        fprintf(fp,"\n%f ",rcenter); 

        for (int i = 1; i <= atom->ntypes; i++)

          for (int j = 1; j <= atom->ntypes; j++)

            if (rdfpair[i][j]) {

              irdf = rdfpair[i][j] - 1;

              fprintf(fp,"%f %f ",gr_ave[irdf][bin],ncoord_ave[irdf][bin]);  

            }  

      }

      fprintf(fp,"\n");

    }

    fflush(fp);

  }

}

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

   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.

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

#ifndef FIX_RDF_H

#define FIX_RDF_H

#include "stdio.h"

#include "fix.h"

namespace LAMMPS_NS {

class FixRDF : public Fix {

 public:

  FixRDF(class LAMMPS *, int, char **);

  ~FixRDF();

  int setmask();

  void init();

  void init_list(int, class NeighList *);

  void setup(int);

  void end_of_step();

 private:

  int me,first;

  FILE *fp;

  int maxbin;			 // # of rdf bins

  int n_rdf_pairs;            	 // # of rdf pairs

  int nframes;                   // # of rdf snapshots taken

  double delr,delrinv;		 // bin width and its inverse

  int **rdfpair;              	 // mapping from 2 types to rdf pair

  int **hist,**hist_all;	 // histogram bins

  int *nrdfatoms;             	 // # of atoms of each type in the group

  double **gr_ave,**ncoord_ave;  // accumulators for average rdf statistics

  class NeighList *list;         // half neighbor list

};

}

#endif