Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/USER-OMP/improper_umbrella_omp.cpp
d3355b03dc0elammm-master

Last Change
Raw File

improper_umbrella_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "improper_umbrella_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
void ImproperUmbrellaOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->nimproperlist;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
if (force->newton_bond) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_bond) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_bond) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
{
int i1,i2,i3,i4,n,type;
double eimproper,f1[3],f2[3],f3[3],f4[3];
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z;
double domega,c,a,s,projhfg,dhax,dhay,dhaz,dahx,dahy,dahz,cotphi;
double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz;
eimproper = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const * const improperlist = neighbor->improperlist;
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = improperlist[n][0];
i2 = improperlist[n][1];
i3 = improperlist[n][2];
i4 = improperlist[n][3];
type = improperlist[n][4];
// 1st bond
vb1x = x[i2][0] - x[i1][0];
vb1y = x[i2][1] - x[i1][1];
vb1z = x[i2][2] - x[i1][2];
domain->minimum_image(vb1x,vb1y,vb1z);
// 2nd bond
vb2x = x[i3][0] - x[i1][0];
vb2y = x[i3][1] - x[i1][1];
vb2z = x[i3][2] - x[i1][2];
domain->minimum_image(vb2x,vb2y,vb2z);
// 3rd bond
vb3x = x[i4][0] - x[i1][0];
vb3y = x[i4][1] - x[i1][1];
vb3z = x[i4][2] - x[i1][2];
domain->minimum_image(vb3x,vb3y,vb3z);
// c0 calculation
// A = vb1 X vb2 is perpendicular to IJK plane
ax = vb1y*vb2z-vb1z*vb2y;
ay = vb1z*vb2x-vb1x*vb2z;
az = vb1x*vb2y-vb1y*vb2x;
ra2 = ax*ax+ay*ay+az*az;
rh2 = vb3x*vb3x+vb3y*vb3y+vb3z*vb3z;
ra = sqrt(ra2);
rh = sqrt(rh2);
if (ra < SMALL) ra = SMALL;
if (rh < SMALL) rh = SMALL;
rar = 1/ra;
rhr = 1/rh;
arx = ax*rar;
ary = ay*rar;
arz = az*rar;
hrx = vb3x*rhr;
hry = vb3y*rhr;
hrz = vb3z*rhr;
c = arx*hrx+ary*hry+arz*hrz;
// error check
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
int me = comm->me;
if (screen) {
char str[128];
sprintf(str,"Improper problem: %d/%d " BIGINT_FORMAT " %d %d %d %d",
me,thr->get_tid(),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) s = 1.0;
if (c < -1.0) s = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
cotphi = c/s;
projhfg = (vb3x*vb1x+vb3y*vb1y+vb3z*vb1z) /
sqrt(vb1x*vb1x+vb1y*vb1y+vb1z*vb1z);
projhfg += (vb3x*vb2x+vb3y*vb2y+vb3z*vb2z) /
sqrt(vb2x*vb2x+vb2y*vb2y+vb2z*vb2z);
if (projhfg > 0.0) {
s *= -1.0;
cotphi *= -1.0;
}
// force and energy
// if w0 = 0: E = k * (1 - cos w)
// if w0 != 0: E = 0.5 * C (cos w - cos w0)^2, C = k/(sin(w0)^2
if (w0[type] == 0.0) {
if (EFLAG) eimproper = kw[type] * (1.0-s);
a = -kw[type];
} else {
domega = s - cos(w0[type]);
a = 0.5 * C[type] * domega;
if (EFLAG) eimproper = a * domega;
a *= 2.0;
}
// dhax = diffrence between H and A in X direction, etc
a = a*cotphi;
dhax = hrx-c*arx;
dhay = hry-c*ary;
dhaz = hrz-c*arz;
dahx = arx-c*hrx;
dahy = ary-c*hry;
dahz = arz-c*hrz;
f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
f4[0] = dahx*rhr;
f4[1] = dahy*rhr;
f4[2] = dahz*rhr;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
f1[2] = -(f2[2] + f3[2] + f4[2]);
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
f[i1][0] += f1[0]*a;
f[i1][1] += f1[1]*a;
f[i1][2] += f1[2]*a;
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2][0] += f3[0]*a;
f[i2][1] += f3[1]*a;
f[i2][2] += f3[2]*a;
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3][0] += f2[0]*a;
f[i3][1] += f2[1]*a;
f[i3][2] += f2[2]*a;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4][0] += f4[0]*a;
f[i4][1] += f4[1]*a;
f[i4][2] += f4[2]*a;
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
c4science · Help