Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/MOLECULE/angle_cosine.cpp
dadf60427b97efficient_neuronet

Last Change
Raw File

angle_cosine.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "angle_cosine.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;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCosine::~AngleCosine()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
}
}
/* ---------------------------------------------------------------------- */
void AngleCosine::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double rsq1,rsq2,r1,r2,c,a,a11,a12,a22;
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];
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];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// c = cosine of angle
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
// force & energy
if (eflag) eangle = k[type]*(1.0+c);
a = k[type];
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// 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);
}
}
/* ---------------------------------------------------------------------- */
void AngleCosine::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(k,n+1,"angle:k");
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void AngleCosine::coeff(int narg, char **arg)
{
if (narg != 2) 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]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleCosine::equilibrium_angle(int i)
{
return MY_PI;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCosine::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCosine::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) fread(&k[1],sizeof(double),atom->nangletypes,fp);
MPI_Bcast(&k[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 AngleCosine::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g\n",i,k[i]);
}
/* ---------------------------------------------------------------------- */
double AngleCosine::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;
return k[type]*(1.0+c);
}
c4science · Help