Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
3d36d38a5183lammm-master

Last Change
Raw File

pair_hbond_dreiding_morse_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_morse_omp.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
PairHbondDreidingMorseOMP::PairHbondDreidingMorseOMP(LAMMPS *lmp) :
PairHbondDreidingMorse(lmp), ThrOMP(lmp, THR_PAIR)
{
respa_enable = 0;
hbcount_thr = hbeng_thr = NULL;
}
/* ---------------------------------------------------------------------- */
PairHbondDreidingMorseOMP::~PairHbondDreidingMorseOMP()
{
respa_enable = 0;
if (hbcount_thr) {
delete[] hbcount_thr;
delete[] hbeng_thr;
}
}
/* ---------------------------------------------------------------------- */
void PairHbondDreidingMorseOMP::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);
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);
}
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 PairHbondDreidingMorseOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,k,m,ii,jj,kk,jnum,itype,jtype,ktype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,rsq1,rsq2,r1,r2;
double factor_hb,force_angle,force_kernel,evdwl;
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 r,dr,dexp,eng_morse,switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
Param *pm;
evdwl = 0.0;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
const int * const type = atom->type;
const double * const special_lj = force->special_lj;
const int * const * const nspecial = atom->nspecial;
const int * const * const special = atom->special;
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;
const int * const klist = special[i];
const int knum = nspecial[i][0];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
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][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
for (kk = 0; kk < knum; kk++) {
k = atom->map(klist[kk]);
if (k < 0) continue;
ktype = type[k];
m = type2param[itype][jtype][ktype];
if (m < 0) continue;
pm = &params[m];
if (rsq < pm->cut_outersq) {
delr1[0] = xtmp - x[k][0];
delr1[1] = ytmp - x[k][1];
delr1[2] = ztmp - x[k][2];
domain->minimum_image(delr1);
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
r1 = sqrt(rsq1);
delr2[0] = x[j][0] - x[k][0];
delr2[1] = x[j][1] - x[k][1];
delr2[2] = x[j][2] - x[k][2];
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;
// Morse-specific kernel
r = sqrt(rsq);
dr = r - pm->r0;
dexp = exp(-pm->alpha * dr);
force_kernel = pm->morse1*(dexp*dexp - dexp)/r * pow(c,pm->ap);
force_angle = pm->ap * eng_morse * pow(c,pm->ap-1)*s;
eng_morse = pm->d0 * (dexp*dexp - 2.0*dexp);
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_morse*switch2;
eng_morse *= switch1;
}
if (EFLAG) {
evdwl = eng_morse * pow(c,params[m].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][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] -= vx1 + vx2;
f[k][1] -= vy1 + vy2;
f[k][2] -= 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][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
}
const int tid = thr->get_tid();
hbcount_thr[tid] = static_cast<double>(hbcount);
hbeng_thr[tid] = hbeng;
}
/* ---------------------------------------------------------------------- */
double PairHbondDreidingMorseOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += comm->nthreads * 2 * sizeof(double);
bytes += PairHbondDreidingMorse::memory_usage();
return bytes;
}
c4science · Help