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angle_charmm_omp.cpp
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Sat, Jun 1, 19:00

angle_charmm_omp.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: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "angle_charmm_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "domain.h"
#include "math_const.h"
#include <math.h>
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
AngleCharmmOMP::AngleCharmmOMP(class LAMMPS *lmp)
: AngleCharmm(lmp), ThrOMP(lmp,THR_ANGLE)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void AngleCharmmOMP::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->nanglelist;
#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);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (inum > 0) {
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);
}
}
thr->timer(Timer::BOND);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_BOND>
void AngleCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
{
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;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const int4_t * _noalias const anglelist = (int4_t *) neighbor->anglelist[0];
const int nlocal = atom->nlocal;
eangle = 0.0;
for (n = nfrom; n < nto; n++) {
i1 = anglelist[n].a;
i2 = anglelist[n].b;
i3 = anglelist[n].c;
type = anglelist[n].t;
// 1st bond
delx1 = x[i1].x - x[i2].x;
dely1 = x[i1].y - x[i2].y;
delz1 = x[i1].z - x[i2].z;
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3].x - x[i2].x;
dely2 = x[i3].y - x[i2].y;
delz2 = x[i3].z - x[i2].z;
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// Urey-Bradley bond
delxUB = x[i3].x - x[i1].x;
delyUB = x[i3].y - x[i1].y;
delzUB = x[i3].z - x[i1].z;
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].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x -= f1[0] + f3[0];
f[i2].y -= f1[1] + f3[1];
f[i2].z -= f1[2] + f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (EVFLAG) ev_tally_thr(this,i1,i2,i3,nlocal,NEWTON_BOND,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2,thr);
}
}

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