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

   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 "compute_rdf.h"

#include "atom.h"

#include "update.h"

#include "force.h"

#include "pair.h"

#include "neighbor.h"

#include "neigh_request.h"

#include "neigh_list.h"

#include "group.h"

#include "memory.h"

#include "error.h"

using namespace LAMMPS_NS;

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

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

  Compute(lmp, narg, arg)

{

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

  array_flag = 1;

  size_array_rows = 1;

  size_array_cols = 1;

  extarray = 1;

  maxbin = atoi(arg[5]);

  npairs = 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 type in compute rdf command");

    npairs++;

    rdfpair[itype][jtype] = npairs;

  }

  hist = memory->create_2d_double_array(maxbin,npairs+1,"rdf:hist");

  array = memory->create_2d_double_array(maxbin,npairs+1,"rdf:array");

  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;

}

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

ComputeRDF::~ComputeRDF()

{

  memory->destroy_2d_int_array(rdfpair);

  memory->destroy_2d_double_array(hist);

  delete [] nrdfatoms;

}

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

void ComputeRDF::init()

{

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

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

  delrinv = 1.0/delr;

  // need an occasional half neighbor list

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

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

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

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

}

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

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

{

  list = ptr;

}

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

void ComputeRDF::compute_array()

{

  invoked_array = update->ntimestep;

  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 < maxbin; i++)

    for (int j = 0; j < npairs; 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[bin][ipair-1]++;

	  if (newton_pair || j < nlocal)

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

	}

      }

    }

  }

  // sum histogram across procs

  MPI_Allreduce(hist[0],array[0],maxbin*npairs,MPI_DOUBLE,MPI_SUM,world);

}

   See the README file in the top-level LAMMPS directory.

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

#ifndef FIX_COM_H

#define FIX_COM_H

#ifndef COMPUTE_RDF_H

#define COMPUTE_RDF_H

#include "stdio.h"

#include "fix.h"

#include "compute.h"

namespace LAMMPS_NS {

class FixCOM : public Fix {

class ComputeRDF : public Compute {

 public:

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

  ~FixCOM();

  int setmask();

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

  ~ComputeRDF();

  void init();

  void setup(int);

  void end_of_step();

  void init_list(int, class NeighList *);

  void compute_array();

 private:

  int me,first;

  FILE *fp;

  double masstotal;

  int first;

  int maxbin;			 // # of rdf bins

  int npairs;            	 // # of rdf pairs

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

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

  double **hist;	         // histogram bins

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

  class NeighList *list;         // half neighbor list

};

}

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

   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 "stdlib.h"

#include "fix_com.h"

#include "atom.h"

#include "update.h"

#include "domain.h"

#include "group.h"

#include "error.h"

using namespace LAMMPS_NS;

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

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

  Fix(lmp, narg, arg)

{

  if (narg != 5) error->all("Illegal fix com command");

  nevery = atoi(arg[3]);

  if (nevery <= 0) error->all("Illegal fix com 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 com file %s",arg[4]);

      error->one(str);

    }

  }

  if (me == 0) {

    fprintf(fp,"# Center-of-mass for group %s\n",group->names[igroup]);

    fprintf(fp,"# TimeStep x y z\n");

  }

}

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

FixCOM::~FixCOM()

{

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

}

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

int FixCOM::setmask()

{

  int mask = 0;

  mask |= END_OF_STEP;

  return mask;

}

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

void FixCOM::init()

{

  masstotal = group->mass(igroup);

}

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

void FixCOM::setup(int vflag)

{

  if (first) end_of_step();

  first = 0;

}

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

void FixCOM::end_of_step()

{

  double xcm[3];

  group->xcm(igroup,masstotal,xcm);

  if (me == 0) {

    fprintf(fp,"%d %g %g %g\n",update->ntimestep,xcm[0],xcm[1],xcm[2]);

    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.

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

#include "stdlib.h"

#include "fix_gyration.h"

#include "atom.h"

#include "update.h"

#include "domain.h"

#include "group.h"

#include "error.h"

using namespace LAMMPS_NS;

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

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

  Fix(lmp, narg, arg)

{

  if (narg != 5) error->all("Illegal fix gyration command");

  nevery = atoi(arg[3]);

  if (nevery <= 0) error->all("Illegal fix gyration 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 gyration file %s",arg[4]);

      error->one(str);

    }

  }

  if (me == 0) {

    fprintf(fp,"# Radius-of-gyration for group %s\n",group->names[igroup]);

    fprintf(fp,"# TimeStep Rg\n");

  }

}

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

FixGyration::~FixGyration()

{

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

}

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

int FixGyration::setmask()

{

  int mask = 0;

  mask |= END_OF_STEP;

  return mask;

}

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

void FixGyration::init()

{

  masstotal = group->mass(igroup);

}

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

void FixGyration::setup(int vflag)

{

  if (first) end_of_step();

  first = 0;

}

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

void FixGyration::end_of_step()

{

  double xcm[3];

  group->xcm(igroup,masstotal,xcm);

  double rg = group->gyration(igroup,masstotal,xcm);

  if (me == 0) {

    fprintf(fp,"%d %g\n",update->ntimestep,rg);

    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_GYRATION_H

#define FIX_GYRATION_H

#include "stdio.h"

#include "fix.h"

namespace LAMMPS_NS {

class FixGyration : public Fix {

 public:

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

  ~FixGyration();

  int setmask();

  void init();

  void setup(int);

  void end_of_step();

 private:

  int me,first;

  FILE *fp;

  double masstotal;

};

}

#endif