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fix_reax_c.cpp
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Fri, Nov 1, 12:24

fix_reax_c.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hasan Metin Aktulga, Purdue University
(now at Lawrence Berkeley National Laboratory, hmaktulga@lbl.gov)
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
------------------------------------------------------------------------- */
#include "fix_reax_c.h"
#include "atom.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define MAX_REAX_BONDS 30
#define MIN_REAX_BONDS 15
#define MIN_REAX_HBONDS 25
/* ---------------------------------------------------------------------- */
FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
// perform initial allocation of atom-based arrays
// register with atom class
num_bonds = NULL;
num_hbonds = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// initialize arrays to MIN so atom migration is OK the 1st time
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
num_bonds[i] = num_hbonds[i] = MIN_REAX_BONDS;
// set comm sizes needed by this fix
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
FixReaxC::~FixReaxC()
{
// unregister this fix so atom class doesn't invoke it any more
atom->delete_callback(id,0);
// delete locally stored arrays
memory->destroy(num_bonds);
memory->destroy(num_hbonds);
}
/* ---------------------------------------------------------------------- */
int FixReaxC::setmask()
{
int mask = 0;
return mask;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixReaxC::memory_usage()
{
int nmax = atom->nmax;
double bytes = nmax * 2 * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixReaxC::grow_arrays(int nmax)
{
memory->grow(num_bonds,nmax,"reaxc:num_bonds");
memory->grow(num_hbonds,nmax,"reaxc:num_hbonds");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixReaxC::copy_arrays(int i, int j, int delflag)
{
num_bonds[j] = num_bonds[i];
num_hbonds[j] = num_hbonds[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixReaxC::pack_exchange(int i, double *buf)
{
buf[0] = num_bonds[i];
buf[1] = num_hbonds[i];
return 2;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixReaxC::unpack_exchange(int nlocal, double *buf)
{
num_bonds[nlocal] = static_cast<int> (buf[0]);
num_hbonds[nlocal] = static_cast<int> (buf[1]);
return 2;
}
/* ---------------------------------------------------------------------- */
int FixReaxC::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = num_bonds[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void FixReaxC::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
num_bonds[i] = static_cast<int> (buf[m++]);
}

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