Commit 284c1f2d authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 209f169c

src/CLASS2/pair_lj_class2_coul_long.h

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

   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 PAIR_LJ_CLASS2_COUL_LONG_H

#define PAIR_LJ_CLASS2_COUL_LONG_H



#include "pair.h"



namespace LAMMPS_NS {



class PairLJClass2CoulLong : public Pair {

 public:

  PairLJClass2CoulLong(class LAMMPS *);

  ~PairLJClass2CoulLong();

  void compute(int, int);

  void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void init_style();

  void write_restart(FILE *);

  void read_restart(FILE *);

  void write_restart_settings(FILE *);

  void read_restart_settings(FILE *);

  void single(int, int, int, int, double, double, double, int, One &);



  void extract_long(double *);



 private:

  double cut_lj_global;

  double **cut_lj,**cut_ljsq;

  double cut_coul,cut_coulsq;

  double **epsilon,**sigma;

  double **lj1,**lj2,**lj3,**lj4,**offset;

  double g_ewald;



  void allocate();

};



}



#endif

src/DPD/atom_vec_dpd.cpp

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

   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 "atom_vec_dpd.h"

#include "atom.h"

#include "domain.h"

#include "modify.h"

#include "fix.h"

#include "memory.h"

#include "error.h"



using namespace LAMMPS_NS;



#define DELTA 10000



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



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

  AtomVecAtomic(lmp, narg, arg)

{

  mass_type = 1;

  comm_x_only = 0;

  size_comm = 6;

  size_reverse = 3;

  size_border = 9;

  size_data_atom = 5;

  size_data_vel = 4;

  xcol_data = 3;

}



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

   zero auxiliary data for n ghost atoms

   data in border(), not including x,tag,type,mask

   grow() is here since zero_ghost called first in hybrid::unpack_border()

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



void AtomVecDPD::zero_ghost(int n, int first)

{

  int last = first + n;

  for (int i = first; i < last; i++) {

    if (i == nmax) atom->avec->grow(0);

    v[i][0] = 0.0;

    v[i][1] = 0.0;

    v[i][2] = 0.0;

  }

}



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



int AtomVecDPD::pack_comm(int n, int *list, double *buf, int *pbc_flags)

{

  int i,j,m;



  m = 0;

  if (pbc_flags[0] == 0) {

    for (i = 0; i < n; i++) {

      j = list[i];

      buf[m++] = x[j][0];

      buf[m++] = x[j][1];

      buf[m++] = x[j][2];

      buf[m++] = v[j][0];

      buf[m++] = v[j][1];

      buf[m++] = v[j][2];

    }

  } else {

    double xprd = domain->xprd;

    double yprd = domain->yprd;

    double zprd = domain->zprd;

    for (i = 0; i < n; i++) {

      j = list[i];

      buf[m++] = x[j][0] + pbc_flags[1]*xprd;

      buf[m++] = x[j][1] + pbc_flags[2]*yprd;

      buf[m++] = x[j][2] + pbc_flags[3]*zprd;

      buf[m++] = v[j][0];

      buf[m++] = v[j][1];

      buf[m++] = v[j][2];

    }

  }

  return m;

}



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



int AtomVecDPD::pack_comm_one(int i, double *buf)

{

  buf[0] = v[i][0];

  buf[1] = v[i][1];

  buf[2] = v[i][2];

  return 3;

}



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



void AtomVecDPD::unpack_comm(int n, int first, double *buf)

{

  int i,m,last;



  m = 0;

  last = first + n;

  for (i = first; i < last; i++) {

    x[i][0] = buf[m++];

    x[i][1] = buf[m++];

    x[i][2] = buf[m++];

    v[i][0] = buf[m++];

    v[i][1] = buf[m++];

    v[i][2] = buf[m++];

  }

}



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



int AtomVecDPD::unpack_comm_one(int i, double *buf)

{

  v[i][0] = buf[0];

  v[i][1] = buf[1];

  v[i][2] = buf[2];

  return 3;

}



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



int AtomVecDPD::pack_border(int n, int *list, double *buf, int *pbc_flags)

{

  int i,j,m;



  m = 0;

  if (pbc_flags[0] == 0) {

    for (i = 0; i < n; i++) {

      j = list[i];

      buf[m++] = x[j][0];

      buf[m++] = x[j][1];

      buf[m++] = x[j][2];

      buf[m++] = tag[j];

      buf[m++] = type[j];

      buf[m++] = mask[j];

      buf[m++] = v[j][0];

      buf[m++] = v[j][1];

      buf[m++] = v[j][2];

   }

  } else {

    double xprd = domain->xprd;

    double yprd = domain->yprd;

    double zprd = domain->zprd;

    for (i = 0; i < n; i++) {

      j = list[i];

      buf[m++] = x[j][0] + pbc_flags[1]*xprd;

      buf[m++] = x[j][1] + pbc_flags[2]*yprd;

      buf[m++] = x[j][2] + pbc_flags[3]*zprd;

      buf[m++] = tag[j];

      buf[m++] = type[j];

      buf[m++] = mask[j];

      buf[m++] = v[j][0];

      buf[m++] = v[j][1];

      buf[m++] = v[j][2];

    }

  }

  return m;

}



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



int AtomVecDPD::pack_border_one(int i, double *buf)

{

  buf[0] = v[i][0];

  buf[1] = v[i][1];

  buf[2] = v[i][2];

  return 3;

}



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



void AtomVecDPD::unpack_border(int n, int first, double *buf)

{

  int i,m,last;



  m = 0;

  last = first + n;

  for (i = first; i < last; i++) {

    if (i == nmax) grow(0);

    x[i][0] = buf[m++];

    x[i][1] = buf[m++];

    x[i][2] = buf[m++];

    tag[i] = static_cast<int> (buf[m++]);

    type[i] = static_cast<int> (buf[m++]);

    mask[i] = static_cast<int> (buf[m++]);

    v[i][0] = buf[m++];

    v[i][1] = buf[m++];

    v[i][2] = buf[m++];

  }

}



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



int AtomVecDPD::unpack_border_one(int i, double *buf)

{

  v[i][0] = buf[0];

  v[i][1] = buf[1];

  v[i][2] = buf[2];

  return 3;

}

src/DPD/atom_vec_dpd.h

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

   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 ATOM_VEC_DPD_H

#define ATOM_VEC_DPD_H



#include "atom_vec_atomic.h"



namespace LAMMPS_NS {



class AtomVecDPD : public AtomVecAtomic {

 public:

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

  void zero_ghost(int, int);

  int pack_comm(int, int *, double *, int *);

  int pack_comm_one(int, double *);

  void unpack_comm(int, int, double *);

  int unpack_comm_one(int, double *);

  int pack_border(int, int *, double *, int *);

  int pack_border_one(int, double *);

  void unpack_border(int, int, double *);

  int unpack_border_one(int, double *);

};



}



#endif

src/GRANULAR/atom_vec_granular.cpp

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src/GRANULAR/atom_vec_granular.h

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

   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 ATOM_VEC_GRANULAR_H

#define ATOM_VEC_GRANULAR_H



#include "atom_vec.h"



namespace LAMMPS_NS {



class AtomVecGranular : public AtomVec {

 public:

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

  ~AtomVecGranular() {}

  void grow(int);

  void reset_ptrs();

  void zero_owned(int);

  void zero_ghost(int, int);

  void copy(int, int);

  int pack_comm(int, int *, double *, int *);

  int pack_comm_one(int, double *);

  void unpack_comm(int, int, double *);

  int unpack_comm_one(int, double *);

  int pack_reverse(int, int, double *);

  int pack_reverse_one(int, double *);

  void unpack_reverse(int, int *, double *);

  int unpack_reverse_one(int, double *);

  int pack_border(int, int *, double *, int *);

  int pack_border_one(int, double *);

  void unpack_border(int, int, double *);

  int unpack_border_one(int, double *);

  int pack_exchange(int, double *);

  int unpack_exchange(double *);

  int size_restart();

  int size_restart_one(int);

  int pack_restart(int, double *);

  int unpack_restart(double *);

  void create_atom(int, double, double, double, int);

  void data_atom(double, double, double, int, char **, int);

  void data_vel(int, char *, int);

  int memory_usage();



 private:

  double PI;

  int *tag,*type,*mask,*image;

  double **x,**v,**f;

  double *radius,*density,*rmass;

  double **phix,**phiv,**phia;

};



}



#endif

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