Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F67482045
angle_dipole.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Jun 22, 16:16
Size
7 KB
Mime Type
text/x-c
Expires
Mon, Jun 24, 16:16 (2 d)
Engine
blob
Format
Raw Data
Handle
18323556
Attached To
rLAMMPS lammps
angle_dipole.cpp
View Options
/* ----------------------------------------------------------------------
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
}
Event Timeline
Log In to Comment