Page MenuHomec4science
Files F81315575

pair_hbond_dreiding_lj_omp.cpp
No OneTemporary
Actions

File Metadata

Created
Thu, Sep 5, 07:48

pair_hbond_dreiding_lj_omp.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 <math.h>
#include "pair_hbond_dreiding_lj_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "math_special.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJOMP::PairHbondDreidingLJOMP(LAMMPS *lmp) :
PairHbondDreidingLJ(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
hbcount_thr = hbeng_thr = NULL;
}
/* ---------------------------------------------------------------------- */
PairHbondDreidingLJOMP::~PairHbondDreidingLJOMP()
{
if (hbcount_thr) {
delete[] hbcount_thr;
delete[] hbeng_thr;
}
}
/* ---------------------------------------------------------------------- */
void PairHbondDreidingLJOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
if (!hbcount_thr) {
hbcount_thr = new double[nthreads];
hbeng_thr = new double[nthreads];
}
for (int i=0; i < nthreads; ++i) {
hbcount_thr[i] = 0.0;
hbeng_thr[i] = 0.0;
}
#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 (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
// reduce per thread hbond data
if (eflag_global) {
pvector[0] = 0.0;
pvector[1] = 0.0;
for (int i=0; i < nthreads; ++i) {
pvector[0] += hbcount_thr[i];
pvector[1] += hbeng_thr[i];
}
}
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairHbondDreidingLJOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,m,ii,jj,kk,jnum,knum,itype,jtype,ktype,iatom,imol;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,rsq1,rsq2,r1,r2;
double factor_hb,force_angle,force_kernel,evdwl,eng_lj;
double c,s,a,b,ac,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;
double fi[3],fj[3],delr1[3],delr2[3];
double r2inv,r10inv;
double switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
const tagint *klist;
evdwl = 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 tagint * _noalias const tag = atom->tag;
const int * _noalias const molindex = atom->molindex;
const int * _noalias const molatom = atom->molatom;
const int * _noalias const type = atom->type;
const double * _noalias const special_lj = force->special_lj;
const int * const * const nspecial = atom->nspecial;
const tagint * const * const special = atom->special;
const int molecular = atom->molecular;
Molecule * const * const onemols = atom->avec->onemols;
double fxtmp,fytmp,fztmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// ii = loop over donors
// jj = loop over acceptors
// kk = loop over hydrogens bonded to donor
int hbcount = 0;
double hbeng = 0.0;
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
itype = type[i];
if (!donor[itype]) continue;
if (molecular == 1) {
klist = special[i];
knum = nspecial[i][0];
} else {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
klist = onemols[imol]->special[iatom];
knum = onemols[imol]->nspecial[iatom][0];
tagprev = tag[i] - iatom - 1;
}
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_hb = special_lj[sbmask(j)];
j &= NEIGHMASK;
jtype = type[j];
if (!acceptor[jtype]) continue;
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
if (molecular == 1) k = atom->map(klist[kk]);
else k = atom->map(klist[kk]+tagprev);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
if (m < 0) continue;
const Param &pm = params[m];
if (rsq < pm.cut_outersq) {
delr1[0] = xtmp - x[k].x;
delr1[1] = ytmp - x[k].y;
delr1[2] = ztmp - x[k].z;
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j].x - x[k].x;
delr2[1] = x[j].y - x[k].y;
delr2[2] = x[j].z - x[k].z;
domain->minimum_image(delr2);
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2];
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
ac = acos(c);
if (ac > pm.cut_angle && ac < (2.0*MY_PI - pm.cut_angle)) {
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
// LJ-specific kernel
r2inv = 1.0/rsq;
r10inv = r2inv*r2inv*r2inv*r2inv*r2inv;
force_kernel = r10inv*(pm.lj1*r2inv - pm.lj2)*r2inv *
powint(c,pm.ap);
force_angle = pm.ap * r10inv*(pm.lj3*r2inv - pm.lj4) *
powint(c,pm.ap-1)*s;
eng_lj = r10inv*(pm.lj3*r2inv - pm.lj4);
if (rsq > pm.cut_innersq) {
switch1 = (pm.cut_outersq-rsq) * (pm.cut_outersq-rsq) *
(pm.cut_outersq + 2.0*rsq - 3.0*pm.cut_innersq) /
pm.denom_vdw;
switch2 = 12.0*rsq * (pm.cut_outersq-rsq) *
(rsq-pm.cut_innersq) / pm.denom_vdw;
force_kernel = force_kernel*switch1 + eng_lj*switch2/rsq;
force_angle *= switch1;
eng_lj *= switch1;
}
if (EFLAG) {
evdwl = eng_lj * powint(c,pm.ap);
evdwl *= factor_hb;
}
a = factor_hb*force_angle/s;
b = factor_hb*force_kernel;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
vx1 = a11*delr1[0] + a12*delr2[0];
vx2 = a22*delr2[0] + a12*delr1[0];
vy1 = a11*delr1[1] + a12*delr2[1];
vy2 = a22*delr2[1] + a12*delr1[1];
vz1 = a11*delr1[2] + a12*delr2[2];
vz2 = a22*delr2[2] + a12*delr1[2];
fi[0] = vx1 + b*delx;
fi[1] = vy1 + b*dely;
fi[2] = vz1 + b*delz;
fj[0] = vx2 - b*delx;
fj[1] = vy2 - b*dely;
fj[2] = vz2 - b*delz;
fxtmp += fi[0];
fytmp += fi[1];
fztmp += fi[2];
f[j].x += fj[0];
f[j].y += fj[1];
f[j].z += fj[2];
f[k].x -= vx1 + vx2;
f[k].y -= vy1 + vy2;
f[k].z -= vz1 + vz2;
// KIJ instead of IJK b/c delr1/delr2 are both with respect to k
if (EVFLAG) ev_tally3_thr(this,k,i,j,evdwl,0.0,fi,fj,delr1,delr2,thr);
if (EFLAG) {
hbcount++;
hbeng += evdwl;
}
}
}
}
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
}
const int tid = thr->get_tid();
hbcount_thr[tid] = static_cast<double>(hbcount);
hbeng_thr[tid] = hbeng;
}
/* ---------------------------------------------------------------------- */
double PairHbondDreidingLJOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += comm->nthreads * 2 * sizeof(double);
bytes += PairHbondDreidingLJ::memory_usage();
return bytes;
}

Event Timeline

c4science · Help