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lammps/src/MOLECULE/angle_cosine_delta.cpp
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angle_cosine_delta.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: Axel Kohlmeyer (Temple U), akohlmey at gmail.com
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_cosine_delta.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCosineDelta::AngleCosineDelta(LAMMPS *lmp) : AngleCosineSquared(lmp) {}
/* ---------------------------------------------------------------------- */
void AngleCosineDelta::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2,theta,dtheta,dcostheta,tk;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,a,cot,a11,a12,a22,b11,b12,b22,c0,s0,s;
eangle = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
theta = acos(c);
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
cot = c/s;
// force & energy
dtheta = theta - theta0[type];
dcostheta = cos(dtheta);
tk = k[type] * (1.0-dcostheta);
if (eflag) eangle = tk;
a = -k[type];
// expand dtheta for cos and sin contribution to force
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
b11 = -a*c*cot / rsq1;
b12 = a*cot / (r1*r2);
b22 = -a*c*cot / rsq2;
c0 = cos(theta0[type]);
s0 = sin(theta0[type]);
f1[0] = (a11*delx1 + a12*delx2)*c0 + (b11*delx1 + b12*delx2)*s0;
f1[1] = (a11*dely1 + a12*dely2)*c0 + (b11*dely1 + b12*dely2)*s0;
f1[2] = (a11*delz1 + a12*delz2)*c0 + (b11*delz1 + b12*delz2)*s0;
f3[0] = (a22*delx2 + a12*delx1)*c0 + (b22*delx2 + b12*delx1)*s0;
f3[1] = (a22*dely2 + a12*dely1)*c0 + (b22*dely2 + b12*dely1)*s0;
f3[2] = (a22*delz2 + a12*delz1)*c0 + (b22*delz2 + b12*delz1)*s0;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
/* ---------------------------------------------------------------------- */
double AngleCosineDelta::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double theta = acos(c);
double dtheta = theta - theta0[type];
double dcostheta = cos(dtheta);
double tk = k[type] * (1.0-dcostheta);
return tk;
}
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