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lammps/src/MOLECULE/dihedral_harmonic.cpp
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dihedral_harmonic.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 <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "dihedral_harmonic.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralHarmonic::DihedralHarmonic(LAMMPS *lmp) : Dihedral(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
DihedralHarmonic::~DihedralHarmonic()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(sign);
memory->destroy(multiplicity);
memory->destroy(cos_shift);
memory->destroy(sin_shift);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHarmonic::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
double c,s,p,sx2,sy2,sz2;
edihedral = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
int **dihedrallist = neighbor->dihedrallist;
int ndihedrallist = neighbor->ndihedrallist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < ndihedrallist; n++) {
i1 = dihedrallist[n][0];
i2 = dihedrallist[n][1];
i3 = dihedrallist[n][2];
i4 = dihedrallist[n][3];
type = dihedrallist[n][4];
// 1st bond
vb1x = x[i1][0] - x[i2][0];
vb1y = x[i1][1] - x[i2][1];
vb1z = x[i1][2] - x[i2][2];
// 2nd bond
vb2x = x[i3][0] - x[i2][0];
vb2y = x[i3][1] - x[i2][1];
vb2z = x[i3][2] - x[i2][2];
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
// 3rd bond
vb3x = x[i4][0] - x[i3][0];
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
// c,s calculation
ax = vb1y*vb2zm - vb1z*vb2ym;
ay = vb1z*vb2xm - vb1x*vb2zm;
az = vb1x*vb2ym - vb1y*vb2xm;
bx = vb3y*vb2zm - vb3z*vb2ym;
by = vb3z*vb2xm - vb3x*vb2zm;
bz = vb3x*vb2ym - vb3y*vb2xm;
rasq = ax*ax + ay*ay + az*az;
rbsq = bx*bx + by*by + bz*bz;
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
rg = sqrt(rgsq);
rginv = ra2inv = rb2inv = 0.0;
if (rg > 0) rginv = 1.0/rg;
if (rasq > 0) ra2inv = 1.0/rasq;
if (rbsq > 0) rb2inv = 1.0/rbsq;
rabinv = sqrt(ra2inv*rb2inv);
c = (ax*bx + ay*by + az*bz)*rabinv;
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
m = multiplicity[type];
p = 1.0;
ddf1 = df1 = 0.0;
for (i = 0; i < m; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
}
p = p*cos_shift[type] + df1*sin_shift[type];
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
df1 *= -m;
p += 1.0;
if (m == 0) {
p = 1.0 + cos_shift[type];
df1 = 0.0;
}
if (eflag) edihedral = k[type] * p;
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
fga = fg*ra2inv*rginv;
hgb = hg*rb2inv*rginv;
gaa = -ra2inv*rg;
gbb = rb2inv*rg;
dtfx = gaa*ax;
dtfy = gaa*ay;
dtfz = gaa*az;
dtgx = fga*ax - hgb*bx;
dtgy = fga*ay - hgb*by;
dtgz = fga*az - hgb*bz;
dthx = gbb*bx;
dthy = gbb*by;
dthz = gbb*bz;
df = -k[type] * df1;
sx2 = df*dtgx;
sy2 = df*dtgy;
sz2 = df*dtgz;
f1[0] = df*dtfx;
f1[1] = df*dtfy;
f1[2] = df*dtfz;
f2[0] = sx2 - f1[0];
f2[1] = sy2 - f1[1];
f2[2] = sz2 - f1[2];
f4[0] = df*dthx;
f4[1] = df*dthy;
f4[2] = df*dthz;
f3[0] = -sx2 - f4[0];
f3[1] = -sy2 - f4[1];
f3[2] = -sz2 - f4[2];
// apply force to each of 4 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] += f2[0];
f[i2][1] += f2[1];
f[i2][2] += f2[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (newton_bond || i4 < nlocal) {
f[i4][0] += f4[0];
f[i4][1] += f4[1];
f[i4][2] += f4[2];
}
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
/* ---------------------------------------------------------------------- */
void DihedralHarmonic::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
memory->create(k,n+1,"dihedral:k");
memory->create(sign,n+1,"dihedral:sign");
memory->create(multiplicity,n+1,"dihedral:multiplicity");
memory->create(cos_shift,n+1,"dihedral:cos_shift");
memory->create(sin_shift,n+1,"dihedral:sin_shift");
memory->create(setflag,n+1,"dihedral:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralHarmonic::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
double k_one = force->numeric(FLERR,arg[1]);
int sign_one = force->inumeric(FLERR,arg[2]);
int multiplicity_one = force->inumeric(FLERR,arg[3]);
// require sign = +/- 1 for backwards compatibility
// arbitrary phase angle shift could be allowed, but would break
// backwards compatibility and is probably not needed
if (sign_one != -1 && sign_one != 1)
error->all(FLERR,"Incorrect sign arg for dihedral coefficients");
if (multiplicity_one < 0)
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
sign[i] = sign_one;
if (sign[i] == 1) {
cos_shift[i] = 1;
sin_shift[i] = 0;
} else {
cos_shift[i] = -1;
sin_shift[i] = 0;
}
multiplicity[i] = multiplicity_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralHarmonic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
}
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
for (int i = 1; i <= atom->ndihedraltypes; i++) {
setflag[i] = 1;
if (sign[i] == 1) {
cos_shift[i] = 1;
sin_shift[i] = 0;
} else {
cos_shift[i] = -1;
sin_shift[i] = 0;
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralHarmonic::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %d %d\n",i,k[i],sign[i],multiplicity[i]);
}
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