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angle_charmm.cpp
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Mon, May 27, 07:28

angle_charmm.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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_charmm.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
/* ---------------------------------------------------------------------- */
AngleCharmm::AngleCharmm(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCharmm::~AngleCharmm()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(theta0);
memory->sfree(k_ub);
memory->sfree(r_ub);
}
}
/* ---------------------------------------------------------------------- */
void AngleCharmm::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 dtheta,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double delxUB,delyUB,delzUB,rsqUB,rUB,dr,rk,forceUB;
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);
// Urey-Bradley bond
delxUB = x[i3][0] - x[i1][0];
delyUB = x[i3][1] - x[i1][1];
delzUB = x[i3][2] - x[i1][2];
domain->minimum_image(delxUB,delyUB,delzUB);
rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;
rUB = sqrt(rsqUB);
// Urey-Bradley force & energy
dr = rUB - r_ub[type];
rk = k_ub[type] * dr;
if (rUB > 0.0) forceUB = -2.0*rk/rUB;
else forceUB = 0.0;
if (eflag) eangle = rk*dr;
// 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;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// harmonic force & energy
dtheta = acos(c) - theta0[type];
tk = k[type] * dtheta;
if (eflag) eangle += tk*dtheta;
a = -2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2 - delxUB*forceUB;
f1[1] = a11*dely1 + a12*dely2 - delyUB*forceUB;
f1[2] = a11*delz1 + a12*delz2 - delzUB*forceUB;
f3[0] = a22*delx2 + a12*delx1 + delxUB*forceUB;
f3[1] = a22*dely2 + a12*dely1 + delyUB*forceUB;
f3[2] = a22*delz2 + a12*delz1 + delzUB*forceUB;
// 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 AngleCharmm::allocate()
{
allocated = 1;
int n = atom->nangletypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k");
theta0 = (double *) memory->smalloc((n+1)*sizeof(double),"angle:theta0");
k_ub = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k_ub");
r_ub = (double *) memory->smalloc((n+1)*sizeof(double),"angle:r_ub");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void AngleCharmm::coeff(int which, int narg, char **arg)
{
if (which > 0) return;
if (narg != 5) error->all("Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double k_one = atof(arg[1]);
double theta0_one = atof(arg[2]);
double k_ub_one = atof(arg[3]);
double r_ub_one = atof(arg[4]);
// convert theta0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
theta0[i] = theta0_one/180.0 * PI;
k_ub[i] = k_ub_one;
r_ub[i] = r_ub_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleCharmm::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleCharmm::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k_ub[1],sizeof(double),atom->nangletypes,fp);
fwrite(&r_ub[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleCharmm::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
fread(&k_ub[1],sizeof(double),atom->nangletypes,fp);
fread(&r_ub[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&r_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleCharmm::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 delxUB = x[i3][0] - x[i1][0];
double delyUB = x[i3][1] - x[i1][1];
double delzUB = x[i3][2] - x[i1][2];
domain->minimum_image(delxUB,delyUB,delzUB);
double rUB = sqrt(delxUB*delxUB + delyUB*delyUB + delzUB*delzUB);
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 dtheta = acos(c) - theta0[type];
double tk = k[type] * dtheta;
double dr = rUB - r_ub[type];
double rk = k_ub[type] * dr;
return (tk*dtheta + rk*dr);
}

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