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lammps/src/USER-MISC/angle_dipole.cpp
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angle_dipole.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 authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_dipole.h"
#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) {}
/* ---------------------------------------------------------------------- */
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;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
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(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
}
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