Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/CLASS2/angle_class2.cpp
354e20f43157lammm-master-deprecated

Last Change
Raw File

angle_class2.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 author: Eric Simon (Cray)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "angle_class2.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
/* ---------------------------------------------------------------------- */
AngleClass2::AngleClass2(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleClass2::~AngleClass2()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(setflag_a);
memory->destroy(setflag_bb);
memory->destroy(setflag_ba);
memory->destroy(theta0);
memory->destroy(k2);
memory->destroy(k3);
memory->destroy(k4);
memory->destroy(bb_k);
memory->destroy(bb_r1);
memory->destroy(bb_r2);
memory->destroy(ba_k1);
memory->destroy(ba_k2);
memory->destroy(ba_r1);
memory->destroy(ba_r2);
}
}
/* ---------------------------------------------------------------------- */
void AngleClass2::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,dtheta2,dtheta3,dtheta4,de_angle;
double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
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);
// 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;
// force & energy for angle term
dtheta = acos(c) - theta0[type];
dtheta2 = dtheta*dtheta;
dtheta3 = dtheta2*dtheta;
dtheta4 = dtheta3*dtheta;
de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
4.0*k4[type]*dtheta3;
a = -de_angle*s;
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;
if (eflag) eangle = k2[type]*dtheta2 + k3[type]*dtheta3 + k4[type]*dtheta4;
// force & energy for bond-bond term
dr1 = r1 - bb_r1[type];
dr2 = r2 - bb_r2[type];
tk1 = bb_k[type] * dr1;
tk2 = bb_k[type] * dr2;
f1[0] -= delx1*tk2/r1;
f1[1] -= dely1*tk2/r1;
f1[2] -= delz1*tk2/r1;
f3[0] -= delx2*tk1/r2;
f3[1] -= dely2*tk1/r2;
f3[2] -= delz2*tk1/r2;
if (eflag) eangle += bb_k[type]*dr1*dr2;
// force & energy for bond-angle term
aa1 = s * dr1 * ba_k1[type];
aa2 = s * dr2 * ba_k2[type];
aa11 = aa1 * c / rsq1;
aa12 = -aa1 / (r1 * r2);
aa21 = aa2 * c / rsq1;
aa22 = -aa2 / (r1 * r2);
vx11 = (aa11 * delx1) + (aa12 * delx2);
vx12 = (aa21 * delx1) + (aa22 * delx2);
vy11 = (aa11 * dely1) + (aa12 * dely2);
vy12 = (aa21 * dely1) + (aa22 * dely2);
vz11 = (aa11 * delz1) + (aa12 * delz2);
vz12 = (aa21 * delz1) + (aa22 * delz2);
aa11 = aa1 * c / rsq2;
aa21 = aa2 * c / rsq2;
vx21 = (aa11 * delx2) + (aa12 * delx1);
vx22 = (aa21 * delx2) + (aa22 * delx1);
vy21 = (aa11 * dely2) + (aa12 * dely1);
vy22 = (aa21 * dely2) + (aa22 * dely1);
vz21 = (aa11 * delz2) + (aa12 * delz1);
vz22 = (aa21 * delz2) + (aa22 * delz1);
b1 = ba_k1[type] * dtheta / r1;
b2 = ba_k2[type] * dtheta / r2;
f1[0] -= vx11 + b1*delx1 + vx12;
f1[1] -= vy11 + b1*dely1 + vy12;
f1[2] -= vz11 + b1*delz1 + vz12;
f3[0] -= vx21 + b2*delx2 + vx22;
f3[1] -= vy21 + b2*dely2 + vy22;
f3[2] -= vz21 + b2*delz2 + vz22;
if (eflag) eangle += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
// 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 AngleClass2::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(theta0,n+1,"angle:theta0");
memory->create(k2,n+1,"angle:k2");
memory->create(k3,n+1,"angle:k3");
memory->create(k4,n+1,"angle:k4");
memory->create(bb_k,n+1,"angle:bb_k");
memory->create(bb_r1,n+1,"angle:bb_r1");
memory->create(bb_r2,n+1,"angle:bb_r2");
memory->create(ba_k1,n+1,"angle:ba_k1");
memory->create(ba_k2,n+1,"angle:ba_k2");
memory->create(ba_r1,n+1,"angle:ba_r1");
memory->create(ba_r2,n+1,"angle:ba_r2");
memory->create(setflag,n+1,"angle:setflag");
memory->create(setflag_a,n+1,"angle:setflag_a");
memory->create(setflag_bb,n+1,"angle:setflag_bb");
memory->create(setflag_ba,n+1,"angle:setflag_ba");
for (int i = 1; i <= n; i++)
setflag[i] = setflag_a[i] = setflag_bb[i] = setflag_ba[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
arg1 = "bb" -> BondBond coeffs
arg1 = "ba" -> BondAngle coeffs
else -> Angle coeffs
------------------------------------------------------------------------- */
void AngleClass2::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);
int count = 0;
if (strcmp(arg[1],"bb") == 0) {
if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients");
double bb_k_one = force->numeric(FLERR,arg[2]);
double bb_r1_one = force->numeric(FLERR,arg[3]);
double bb_r2_one = force->numeric(FLERR,arg[4]);
for (int i = ilo; i <= ihi; i++) {
bb_k[i] = bb_k_one;
bb_r1[i] = bb_r1_one;
bb_r2[i] = bb_r2_one;
setflag_bb[i] = 1;
count++;
}
} else if (strcmp(arg[1],"ba") == 0) {
if (narg != 6) error->all(FLERR,"Incorrect args for angle coefficients");
double ba_k1_one = force->numeric(FLERR,arg[2]);
double ba_k2_one = force->numeric(FLERR,arg[3]);
double ba_r1_one = force->numeric(FLERR,arg[4]);
double ba_r2_one = force->numeric(FLERR,arg[5]);
for (int i = ilo; i <= ihi; i++) {
ba_k1[i] = ba_k1_one;
ba_k2[i] = ba_k2_one;
ba_r1[i] = ba_r1_one;
ba_r2[i] = ba_r2_one;
setflag_ba[i] = 1;
count++;
}
} else {
if (narg != 5) error->all(FLERR,"Incorrect args for angle coefficients");
double theta0_one = force->numeric(FLERR,arg[1]);
double k2_one = force->numeric(FLERR,arg[2]);
double k3_one = force->numeric(FLERR,arg[3]);
double k4_one = force->numeric(FLERR,arg[4]);
// convert theta0 from degrees to radians
for (int i = ilo; i <= ihi; i++) {
theta0[i] = theta0_one/180.0 * MY_PI;
k2[i] = k2_one;
k3[i] = k3_one;
k4[i] = k4_one;
setflag_a[i] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
for (int i = ilo; i <= ihi; i++)
if (setflag_a[i] == 1 && setflag_bb[i] == 1 && setflag_ba[i] == 1)
setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleClass2::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleClass2::write_restart(FILE *fp)
{
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k2[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k3[1],sizeof(double),atom->nangletypes,fp);
fwrite(&k4[1],sizeof(double),atom->nangletypes,fp);
fwrite(&bb_k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
fwrite(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
fwrite(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
fwrite(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
fwrite(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
fwrite(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleClass2::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
fread(&k2[1],sizeof(double),atom->nangletypes,fp);
fread(&k3[1],sizeof(double),atom->nangletypes,fp);
fread(&k4[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r2[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k3[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&k4[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb_k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb_r1[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&bb_r2[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ba_k1[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ba_k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ba_r1[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&ba_r2[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 AngleClass2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",
i,theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i]);
fprintf(fp,"\nBondBond Coeffs\n\n");
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g %g %g\n",i,bb_k[i],bb_r1[i],bb_r2[i]);
fprintf(fp,"\nBondAngle Coeffs\n\n");
for (int i = 1; i <= atom->nangletypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,ba_k1[i],ba_k2[i],ba_r1[i],ba_r2[i]);
}
/* ---------------------------------------------------------------------- */
double AngleClass2::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 s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
double dtheta = acos(c) - theta0[type];
double dtheta2 = dtheta*dtheta;
double dtheta3 = dtheta2*dtheta;
double dtheta4 = dtheta3*dtheta;
double energy = k2[type]*dtheta2 + k3[type]*dtheta3 + k4[type]*dtheta4;
double dr1 = r1 - bb_r1[type];
double dr2 = r2 - bb_r2[type];
energy += bb_k[type]*dr1*dr2;
energy += ba_k1[type]*dr1*dtheta + ba_k2[type]*dr2*dtheta;
return energy;
}
c4science · Help