lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
------------------------------------------------------------------------- */

#include "angle_dipole.h"
#include <mpi.h>
#include <cmath>
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;
using namespace MathConst;

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

AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp)
{
  k = NULL;
  gamma0 = NULL;
}

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

AngleDipole::~AngleDipole()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(k);
    memory->destroy(gamma0);
  }
}

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

void AngleDipole::compute(int eflag, int vflag)
{
  int iRef,iDip,iDummy,n,type;
  double delx,dely,delz;
  double eangle,tangle,fi[3],fj[3];
  double r,cosGamma,deltaGamma,kdg,rmu;

  eangle = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x; // position vector
  double **mu = atom->mu; // point-dipole components and moment magnitude
  double **torque = atom->torque;
  int **anglelist = neighbor->anglelist;
  int nanglelist = neighbor->nanglelist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  double **f = atom->f;
  double delTx, delTy, delTz;
  double fx, fy, fz, fmod, fmod_sqrtff;

  if (!newton_bond)
    error->all(FLERR,"'newton' flag for bonded interactions must be 'on'");

  for (n = 0; n < nanglelist; n++) {
    iDip = anglelist[n][0]; // dipole whose orientation is to be restrained
    iRef = anglelist[n][1]; // reference atom toward which dipole will point
    iDummy = anglelist[n][2]; // dummy atom - irrelevant to the interaction
    type = anglelist[n][3];

    delx = x[iRef][0] - x[iDip][0];
    dely = x[iRef][1] - x[iDip][1];
    delz = x[iRef][2] - x[iDip][2];

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

    rmu = r * mu[iDip][3];
    cosGamma = (mu[iDip][0]*delx+mu[iDip][1]*dely+mu[iDip][2]*delz) / rmu;
    deltaGamma = cosGamma - cos(gamma0[type]);
    kdg = k[type] * deltaGamma;

    if (eflag) eangle = kdg * deltaGamma; // energy

    tangle = 2.0 * kdg / rmu;

    delTx = tangle * (dely*mu[iDip][2] - delz*mu[iDip][1]);
    delTy = tangle * (delz*mu[iDip][0] - delx*mu[iDip][2]);
    delTz = tangle * (delx*mu[iDip][1] - dely*mu[iDip][0]);

    torque[iDip][0] += delTx;
    torque[iDip][1] += delTy;
    torque[iDip][2] += delTz;

    // Force couple that counterbalances dipolar torque
    fx = dely*delTz - delz*delTy; // direction (fi): - r x (-T)
    fy = delz*delTx - delx*delTz;
    fz = delx*delTy - dely*delTx;

    fmod = sqrt(delTx*delTx + delTy*delTy + delTz*delTz) / r; // magnitude
    fmod_sqrtff = fmod / sqrt(fx*fx + fy*fy + fz*fz);

    fi[0] = fx * fmod_sqrtff;
    fi[1] = fy * fmod_sqrtff;
    fi[2] = fz * fmod_sqrtff;

    fj[0] = -fi[0];
    fj[1] = -fi[1];
    fj[2] = -fi[2];

    f[iDip][0] += fj[0];
    f[iDip][1] += fj[1];
    f[iDip][2] += fj[2];

    f[iRef][0] += fi[0];
    f[iRef][1] += fi[1];
    f[iRef][2] += fi[2];

    if (evflag) // virial = rij.fi = 0 (fj = -fi & fk = 0)
      ev_tally(iRef,iDip,iDummy,nlocal,newton_bond,eangle,fj,fi,
               0.0,0.0,0.0,0.0,0.0,0.0);
  }
}

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

void AngleDipole::allocate()
{
  allocated = 1;
  int n = atom->nangletypes;

  memory->create(k,n+1,"angle:k");
  memory->create(gamma0,n+1,"angle:gamma0");

  memory->create(setflag,n+1,"angle:setflag");
  for (int i = 1; i <= n; i++) setflag[i] = 0;
}

/* ----------------------------------------------------------------------
   set coeffs for one or more types
------------------------------------------------------------------------- */

void AngleDipole::coeff(int narg, char **arg)
{
  if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients");
  if (!allocated) allocate();

  int ilo,ihi;
  force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi);

  double k_one = force->numeric(FLERR,arg[1]);
  double gamma0_one = force->numeric(FLERR,arg[2]);

  // convert gamma0 from degrees to radians

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    k[i] = k_one;
    gamma0[i] = gamma0_one/180.0 * MY_PI;
    setflag[i] = 1;
    count++;
  }

  if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}

/* ----------------------------------------------------------------------
   used by SHAKE
------------------------------------------------------------------------- */

double AngleDipole::equilibrium_angle(int i)
{
  return gamma0[i];
}

/* ----------------------------------------------------------------------
   proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */

void AngleDipole::write_restart(FILE *fp)
{
  fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
  fwrite(&gamma0[1],sizeof(double),atom->nangletypes,fp);
}

/* ----------------------------------------------------------------------
   proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */

void AngleDipole::read_restart(FILE *fp)
{
  allocate();

  if (comm->me == 0) {
    fread(&k[1],sizeof(double),atom->nangletypes,fp);
    fread(&gamma0[1],sizeof(double),atom->nangletypes,fp);
  }
  MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
  MPI_Bcast(&gamma0[1],atom->nangletypes,MPI_DOUBLE,0,world);

  for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}

/* ----------------------------------------------------------------------
   proc 0 writes to data file
------------------------------------------------------------------------- */

void AngleDipole::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->nangletypes; i++)
    fprintf(fp,"%d %g %g\n",i,k[i],gamma0[i]);
}

/* ----------------------------------------------------------------------
   used by ComputeAngleLocal
------------------------------------------------------------------------- */

double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
{
  double **x = atom->x; // position vector
  double **mu = atom->mu; // point-dipole components and moment magnitude

  double delx = x[iRef][0] - x[iDip][0];
  double dely = x[iRef][1] - x[iDip][1];
  double delz = x[iRef][2] - x[iDip][2];

  domain->minimum_image(delx,dely,delz);

  double r = sqrt(delx*delx + dely*dely + delz*delz);
  double rmu = r * mu[iDip][3];
  double cosGamma = (mu[iDip][0]*delx+mu[iDip][1]*dely+mu[iDip][2]*delz) / rmu;
  double deltaGamma = cosGamma - cos(gamma0[type]);
  double kdg = k[type] * deltaGamma;

  return kdg * deltaGamma; // energy
}