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dihedral_charmm_omp.cpp
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Sun, Nov 10, 15:33

dihedral_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 <mpi.h>
#include <math.h>
#include "dihedral_charmm_omp.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "update.h"
#include "error.h"
#include "suffix.h"
using namespace LAMMPS_NS;
#define TOLERANCE 0.05
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
DihedralCharmmOMP::DihedralCharmmOMP(class LAMMPS *lmp)
: DihedralCharmm(lmp), ThrOMP(lmp,THR_DIHEDRAL|THR_CHARMM)
{
suffix_flag |= Suffix::OMP;
}
/* ---------------------------------------------------------------------- */
void DihedralCharmmOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = 0;
// insure pair->ev_tally() will use 1-4 virial contribution
if (weightflag && vflag_global == 2)
force->pair->vflag_either = force->pair->vflag_global = 1;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = neighbor->ndihedrallist;
#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 DihedralCharmmOMP::eval(int nfrom, int nto, ThrData * const thr)
{
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;
int itype,jtype;
double delx,dely,delz,rsq,r2inv,r6inv;
double forcecoul,forcelj,fpair,ecoul,evdwl;
ecoul = evdwl = edihedral = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
const double * _noalias const q = atom->q;
const int * const atomtype = atom->type;
const int5_t * _noalias const dihedrallist = (int5_t *) neighbor->dihedrallist[0];
const double qqrd2e = force->qqrd2e;
const int nlocal = atom->nlocal;
for (n = nfrom; n < nto; n++) {
i1 = dihedrallist[n].a;
i2 = dihedrallist[n].b;
i3 = dihedrallist[n].c;
i4 = dihedrallist[n].d;
type = dihedrallist[n].t;
// 1st bond
vb1x = x[i1].x - x[i2].x;
vb1y = x[i1].y - x[i2].y;
vb1z = x[i1].z - x[i2].z;
// 2nd bond
vb2x = x[i3].x - x[i2].x;
vb2y = x[i3].y - x[i2].y;
vb2z = x[i3].z - x[i2].z;
vb2xm = -vb2x;
vb2ym = -vb2y;
vb2zm = -vb2z;
// 3rd bond
vb3x = x[i4].x - x[i3].x;
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
// 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 = comm->me;
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d/%d " BIGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT,
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].x,x[i1].y,x[i1].z);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2].x,x[i2].y,x[i2].z);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3].x,x[i3].y,x[i3].z);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4].x,x[i4].y,x[i4].z);
}
}
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].x += f1[0];
f[i1].y += f1[1];
f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
f[i2].x += f2[0];
f[i2].y += f2[1];
f[i2].z += f2[2];
}
if (NEWTON_BOND || i3 < nlocal) {
f[i3].x += f3[0];
f[i3].y += f3[1];
f[i3].z += f3[2];
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x += f4[0];
f[i4].y += f4[1];
f[i4].z += f4[2];
}
if (EVFLAG)
ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,edihedral,f1,f3,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
// 1-4 LJ and Coulomb interactions
// tally energy/virial in pair, using newton_bond as newton flag
if (weight[type] > 0.0) {
itype = atomtype[i1];
jtype = atomtype[i4];
delx = x[i1].x - x[i4].x;
dely = x[i1].y - x[i4].y;
delz = x[i1].z - x[i4].z;
rsq = delx*delx + dely*dely + delz*delz;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
else forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
if (EFLAG) {
ecoul = weight[type] * forcecoul;
evdwl = r6inv * (lj14_3[itype][jtype]*r6inv - lj14_4[itype][jtype]);
evdwl *= weight[type];
}
if (NEWTON_BOND || i1 < nlocal) {
f[i1].x += delx*fpair;
f[i1].y += dely*fpair;
f[i1].z += delz*fpair;
}
if (NEWTON_BOND || i4 < nlocal) {
f[i4].x -= delx*fpair;
f[i4].y -= dely*fpair;
f[i4].z -= delz*fpair;
}
if (EVFLAG) ev_tally_thr(force->pair,i1,i4,nlocal,NEWTON_BOND,
evdwl,ecoul,fpair,delx,dely,delz,thr);
}
}
}

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