lammps/src/bond.cpp

/* ----------------------------------------------------------------------
   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 "string.h"
#include "bond.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

/* -----------------------------------------------------------------------
   set bond contribution to Vdwl energy to 0.0
   a particular bond style can override this
------------------------------------------------------------------------- */

Bond::Bond(LAMMPS *lmp) : Pointers(lmp)
{
  energy = 0.0;

  allocated = 0;

  maxeatom = maxvatom = 0;
  eatom = NULL;
  vatom = NULL;
}

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

Bond::~Bond()
{
  memory->sfree(eatom);
  memory->destroy(vatom);
}

/* ----------------------------------------------------------------------
   check if all coeffs are set
------------------------------------------------------------------------- */

void Bond::init()
{
  if (!allocated) error->all("Bond coeffs are not set");
  for (int i = 1; i <= atom->nbondtypes; i++)
    if (setflag[i] == 0) error->all("All bond coeffs are not set");
  init_style();
}

/* ----------------------------------------------------------------------
   setup for energy, virial computation
   see integrate::ev_set() for values of eflag (0-3) and vflag (0-6)
------------------------------------------------------------------------- */

void Bond::ev_setup(int eflag, int vflag)
{
  int i,n;

  evflag = 1;

  eflag_either = eflag;
  eflag_global = eflag % 2;
  eflag_atom = eflag / 2;

  vflag_either = vflag;
  vflag_global = vflag % 4;
  vflag_atom = vflag / 4;
  
  // reallocate per-atom arrays if necessary

  if (eflag_atom && atom->nmax > maxeatom) {
    maxeatom = atom->nmax;
    memory->sfree(eatom);
    eatom = (double *) memory->smalloc(maxeatom*sizeof(double),"bond:eatom");
  }
  if (vflag_atom && atom->nmax > maxvatom) {
    maxvatom = atom->nmax;
    memory->destroy(vatom);
    memory->create(vatom,maxvatom,6,"bond:vatom");
  }

  // zero accumulators

  if (eflag_global) energy = 0.0;
  if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
  if (eflag_atom) {
    n = atom->nlocal;
    if (force->newton_bond) n += atom->nghost;
    for (i = 0; i < n; i++) eatom[i] = 0.0;
  }
  if (vflag_atom) {
    n = atom->nlocal;
    if (force->newton_bond) n += atom->nghost;
    for (i = 0; i < n; i++) {
      vatom[i][0] = 0.0;
      vatom[i][1] = 0.0;
      vatom[i][2] = 0.0;
      vatom[i][3] = 0.0;
      vatom[i][4] = 0.0;
      vatom[i][5] = 0.0;
    }
  }
}

/* ----------------------------------------------------------------------
   tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */

void Bond::ev_tally(int i, int j, int nlocal, int newton_bond,
		    double ebond, double fbond,
		    double delx, double dely, double delz)
{
  double ebondhalf,v[6];

  if (eflag_either) {
    if (eflag_global) {
      if (newton_bond) energy += ebond;
      else {
	ebondhalf = 0.5*ebond;
	if (i < nlocal) energy += ebondhalf;
	if (j < nlocal) energy += ebondhalf;
      }
    }
    if (eflag_atom) {
      ebondhalf = 0.5*ebond;
      if (newton_bond || i < nlocal) eatom[i] += ebondhalf;
      if (newton_bond || j < nlocal) eatom[j] += ebondhalf;
    }
  }

  if (vflag_either) {
    v[0] = delx*delx*fbond;
    v[1] = dely*dely*fbond;
    v[2] = delz*delz*fbond;
    v[3] = delx*dely*fbond;
    v[4] = delx*delz*fbond;
    v[5] = dely*delz*fbond;

    if (vflag_global) {
      if (newton_bond) {
	virial[0] += v[0];
	virial[1] += v[1];
	virial[2] += v[2];
	virial[3] += v[3];
	virial[4] += v[4];
	virial[5] += v[5];
      } else {
	if (i < nlocal) {
	  virial[0] += 0.5*v[0];
	  virial[1] += 0.5*v[1];
	  virial[2] += 0.5*v[2];
	  virial[3] += 0.5*v[3];
	  virial[4] += 0.5*v[4];
	  virial[5] += 0.5*v[5];
	}
	if (j < nlocal) {
	  virial[0] += 0.5*v[0];
	  virial[1] += 0.5*v[1];
	  virial[2] += 0.5*v[2];
	  virial[3] += 0.5*v[3];
	  virial[4] += 0.5*v[4];
	  virial[5] += 0.5*v[5];
	}
      }
    }

    if (vflag_atom) {
      if (newton_bond || i < nlocal) {
	vatom[i][0] += 0.5*v[0];
	vatom[i][1] += 0.5*v[1];
	vatom[i][2] += 0.5*v[2];
	vatom[i][3] += 0.5*v[3];
	vatom[i][4] += 0.5*v[4];
	vatom[i][5] += 0.5*v[5];
      }
      if (newton_bond || j < nlocal) {
	vatom[j][0] += 0.5*v[0];
	vatom[j][1] += 0.5*v[1];
	vatom[j][2] += 0.5*v[2];
	vatom[j][3] += 0.5*v[3];
	vatom[j][4] += 0.5*v[4];
	vatom[j][5] += 0.5*v[5];
      }
    }
  }
}

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

double Bond::memory_usage()
{
  double bytes = maxeatom * sizeof(double);
  bytes += maxvatom*6 * sizeof(double);
  return bytes;
}