forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8892 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
7eb3ccf732
commit
192ba5588f
|
|
@ -0,0 +1,229 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_buck_long_coul_long_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "math_vector.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBuckLongCoulLongOMP::PairBuckLongCoulLongOMP(LAMMPS *lmp) :
|
||||
PairBuckLongCoulLong(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
cut_respa = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairBuckLongCoulLongOMP::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 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
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairBuckLongCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
double evdwl,ecoul,fpair;
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
const double *x0 = x[0];
|
||||
double *f0 = f[0], *fi = f0;
|
||||
|
||||
int *ilist = list->ilist;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
int i, ii, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
|
||||
int *jneigh, *jneighn, typei, typej, ni;
|
||||
double qi, qri, *cutsqi, *cut_bucksqi,
|
||||
*buck1i, *buck2i, *buckai, *buckci, *rhoinvi, *offseti;
|
||||
double r, rsq, r2inv, force_coul, force_buck;
|
||||
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
|
||||
vector xi, d;
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
|
||||
i = ilist[ii]; fi = f0+3*i;
|
||||
if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
|
||||
offseti = offset[typei = type[i]];
|
||||
buck1i = buck1[typei]; buck2i = buck2[typei];
|
||||
buckai = buck_a[typei]; buckci = buck_c[typei], rhoinvi = rhoinv[typei];
|
||||
cutsqi = cutsq[typei]; cut_bucksqi = cut_bucksq[typei];
|
||||
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
||||
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
|
||||
|
||||
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||
j = *jneigh;
|
||||
ni = sbmask(j);
|
||||
j &= NEIGHMASK;
|
||||
|
||||
{ const register double *xj = x0+(j+(j<<1));
|
||||
d[0] = xi[0] - xj[0]; // pair vector
|
||||
d[1] = xi[1] - xj[1];
|
||||
d[2] = xi[2] - xj[2]; }
|
||||
|
||||
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
|
||||
if (order1 && (rsq < cut_coulsq)) { // coulombic
|
||||
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
|
||||
register double x = g_ewald*r;
|
||||
register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
|
||||
if (ni == 0) {
|
||||
s *= g_ewald*exp(-x*x);
|
||||
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
|
||||
if (EFLAG) ecoul = t;
|
||||
} else { // special case
|
||||
register double f = s*(1.0-special_coul[ni])/r;
|
||||
s *= g_ewald*exp(-x*x);
|
||||
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
|
||||
if (EFLAG) ecoul = t-f;
|
||||
} // table real space
|
||||
} else {
|
||||
register union_int_float_t t;
|
||||
t.f = rsq;
|
||||
register const int k = (t.i & ncoulmask) >> ncoulshiftbits;
|
||||
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
|
||||
if (ni == 0) {
|
||||
force_coul = qiqj*(ftable[k]+f*dftable[k]);
|
||||
if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
|
||||
}
|
||||
else { // special case
|
||||
t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
|
||||
force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
|
||||
if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
|
||||
}
|
||||
}
|
||||
} else force_coul = ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_bucksqi[typej]) { // buckingham
|
||||
register double rn = r2inv*r2inv*r2inv,
|
||||
expr = exp(-r*rhoinvi[typej]);
|
||||
if (order6) { // long-range
|
||||
register double x2 = g2*rsq, a2 = 1.0/x2;
|
||||
x2 = a2*exp(-x2)*buckci[typej];
|
||||
if (ni == 0) {
|
||||
force_buck =
|
||||
r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
|
||||
if (EFLAG) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
|
||||
} else { // special case
|
||||
register double f = special_lj[ni], t = rn*(1.0-f);
|
||||
force_buck = f*r*expr*buck1i[typej]-
|
||||
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
|
||||
if (EFLAG) evdwl = f*expr*buckai[typej] -
|
||||
g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
|
||||
}
|
||||
} else { // cut
|
||||
if (ni == 0) {
|
||||
force_buck = r*expr*buck1i[typej]-rn*buck2i[typej];
|
||||
if (EFLAG) evdwl = expr*buckai[typej] -
|
||||
rn*buckci[typej]-offseti[typej];
|
||||
} else { // special case
|
||||
register double f = special_lj[ni];
|
||||
force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
|
||||
if (EFLAG)
|
||||
evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
|
||||
}
|
||||
}
|
||||
} else force_buck = evdwl = 0.0;
|
||||
|
||||
fpair = (force_coul+force_buck)*r2inv;
|
||||
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
register double *fj = f0+(j+(j<<1)), f;
|
||||
fi[0] += f = d[0]*fpair; fj[0] -= f;
|
||||
fi[1] += f = d[1]*fpair; fj[1] -= f;
|
||||
fi[2] += f = d[2]*fpair; fj[2] -= f;
|
||||
} else {
|
||||
fi[0] += d[0]*fpair;
|
||||
fi[1] += d[1]*fpair;
|
||||
fi[2] += d[2]*fpair;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairBuckLongCoulLongOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairBuckLongCoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(buck/disp/coul/long/omp,PairBuckDispCoulLongOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BUCK_DISP_COUL_LONG_OMP_H
|
||||
#define LMP_PAIR_BUCK_DISP_COUL_LONG_OMP_H
|
||||
|
||||
#include "pair_buck_disp_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBuckDispCoulLongOMP : public PairBuckDispCoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairBuckDispCoulLongOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,259 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_charmm_coul_long_proxy_omp.h"
|
||||
#include "pppm_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCharmmCoulLongProxyOMP::PairLJCharmmCoulLongProxyOMP(LAMMPS *lmp) :
|
||||
PairLJCharmmCoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
proxyflag = 1;
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCharmmCoulLongProxyOMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
kspace = static_cast<PPPMProxy *>(force->kspace);
|
||||
|
||||
PairLJCharmmCoulLong::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCharmmCoulLongProxyOMP::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 defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJCharmmCoulLongProxyOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction,table;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
double philj,switch1,switch2;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
jtype = type[j];
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
if (rsq > cut_lj_innersq) {
|
||||
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
||||
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
||||
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
|
||||
(rsq-cut_lj_innersq) / denom_lj;
|
||||
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
|
||||
forcelj = forcelj*switch1 + philj*switch2;
|
||||
}
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
if (rsq > cut_lj_innersq) {
|
||||
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
||||
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
||||
evdwl *= switch1;
|
||||
}
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCharmmCoulLongProxyOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCharmmCoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/charmm/coul/long/proxy/omp,PairLJCharmmCoulLongProxyOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CHARMM_COUL_LONG_PROXY_OMP_H
|
||||
#define LMP_PAIR_LJ_CHARMM_COUL_LONG_PROXY_OMP_H
|
||||
|
||||
#include "pair_lj_charmm_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCharmmCoulLongProxyOMP :
|
||||
public PairLJCharmmCoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCharmmCoulLongProxyOMP(class LAMMPS *);
|
||||
virtual ~PairLJCharmmCoulLongProxyOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
|
||||
class PPPMProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,226 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_class2_coul_long_proxy_omp.h"
|
||||
#include "pppm_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJClass2CoulLongProxyOMP::PairLJClass2CoulLongProxyOMP(LAMMPS *lmp) :
|
||||
PairLJClass2CoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
proxyflag = 1;
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongProxyOMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
kspace = static_cast<PPPMProxy *>(force->kspace);
|
||||
|
||||
PairLJClass2CoulLong::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJClass2CoulLongProxyOMP::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 defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJClass2CoulLongProxyOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double r,rsq,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
rinv = sqrt(r2inv);
|
||||
r3inv = r2inv*rinv;
|
||||
r6inv = r3inv*r3inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJClass2CoulLongProxyOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJClass2CoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/class2/coul/long/proxy/omp,PairLJClass2CoulLongProxyOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CLASS2_COUL_LONG_PROXY_OMP_H
|
||||
#define LMP_PAIR_LJ_CLASS2_COUL_LONG_PROXY_OMP_H
|
||||
|
||||
#include "pair_lj_class2_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJClass2CoulLongProxyOMP :
|
||||
public PairLJClass2CoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJClass2CoulLongProxyOMP(class LAMMPS *);
|
||||
virtual ~PairLJClass2CoulLongProxyOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
|
||||
class PPPMProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,244 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_coul_long_proxy_omp.h"
|
||||
#include "pppm_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulLongProxyOMP::PairLJCutCoulLongProxyOMP(LAMMPS *lmp) :
|
||||
PairLJCutCoulLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
proxyflag = 1;
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulLongProxyOMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
kspace = static_cast<PPPMProxy *>(force->kspace);
|
||||
|
||||
PairLJCutCoulLong::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulLongProxyOMP::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 defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJCutCoulLongProxyOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction,table;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulLongProxyOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutCoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/long/proxy/omp,PairLJCutCoulLongProxyOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_LONG_PROXY_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_LONG_PROXY_OMP_H
|
||||
|
||||
#include "pair_lj_cut_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulLongProxyOMP : public PairLJCutCoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutCoulLongProxyOMP(class LAMMPS *);
|
||||
virtual ~PairLJCutCoulLongProxyOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
|
||||
class PPPMProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,513 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_tip4p_long_omp.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongOMP::PairLJCutTIP4PLongOMP(LAMMPS *lmp) :
|
||||
PairLJCutTIP4PLong(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
|
||||
// TIP4P cannot compute virial as F dot r
|
||||
// due to finding bonded H atoms which are not near O atom
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
const int nall = nlocal + atom->nghost;
|
||||
|
||||
// reallocate hneigh & newsite if necessary
|
||||
// initialize hneigh[0] to -1 on steps when reneighboring occurred
|
||||
// initialize hneigh[2] to 0 every step
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = atom->nmax;
|
||||
memory->destroy(hneigh);
|
||||
memory->create(hneigh,nmax,3,"pair:hneigh");
|
||||
memory->destroy(newsite);
|
||||
memory->create(newsite,nmax,3,"pair:newsite");
|
||||
}
|
||||
|
||||
// XXX: this could be threaded, too.
|
||||
int i;
|
||||
if (neighbor->ago == 0)
|
||||
for (i = 0; i < nall; i++) hneigh[i][0] = -1;
|
||||
for (i = 0; i < nall; i++) hneigh[i][2] = 0;
|
||||
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#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 (!ncoultablebits) {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<1,0,0,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
|
||||
else eval<0,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
|
||||
else eval<0,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<0,0,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int CTABLE, int EVFLAG, int EFLAG, int VFLAG>
|
||||
void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
int n,vlist[6];
|
||||
int iH1,iH2,jH1,jH2;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
|
||||
double fraction,table;
|
||||
double delxOM,delyOM,delzOM;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
|
||||
double factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc,ddotf;
|
||||
double v[6],xH1[3],xH2[3];
|
||||
double fdx,fdy,fdz,f1x,f1y,f1z,fOx,fOy,fOz,fHx,fHy,fHz;
|
||||
const double *x1,*x2;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const int tid = thr->get_tid();
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
const double cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
|
||||
// if atom I = water O, set x1 = offset charge site
|
||||
// else x1 = x of atom I
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (itype == typeO) {
|
||||
if (hneigh[i][0] < 0) {
|
||||
iH1 = atom->map(atom->tag[i] + 1);
|
||||
iH2 = atom->map(atom->tag[i] + 2);
|
||||
if (iH1 == -1 || iH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
hneigh[i][1] = iH2;
|
||||
hneigh[i][0] = iH1;
|
||||
} else {
|
||||
iH1 = hneigh[i][0];
|
||||
iH2 = hneigh[i][1];
|
||||
if (hneigh[i][2] == 0) {
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
}
|
||||
}
|
||||
x1 = newsite[i];
|
||||
} else x1 = x[i];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// LJ interaction based on true rsq
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj * r2inv;
|
||||
|
||||
fxtmp += delx*forcelj;
|
||||
fytmp += dely*forcelj;
|
||||
fztmp += delz*forcelj;
|
||||
f[j][0] -= delx*forcelj;
|
||||
f[j][1] -= dely*forcelj;
|
||||
f[j][2] -= delz*forcelj;
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
|
||||
evdwl,0.0,forcelj,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
// adjust rsq and delxyz for off-site O charge(s) if necessary
|
||||
// but only if they are within reach
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (rsq < cut_coulsqplus) {
|
||||
if (itype == typeO || jtype == typeO) {
|
||||
|
||||
// if atom J = water O, set x2 = offset charge site
|
||||
// else x2 = x of atom J
|
||||
|
||||
if (jtype == typeO) {
|
||||
if (hneigh[j][0] < 0) {
|
||||
jH1 = atom->map(atom->tag[j] + 1);
|
||||
jH2 = atom->map(atom->tag[j] + 2);
|
||||
if (jH1 == -1 || jH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
hneigh[j][1] = jH2;
|
||||
hneigh[j][0] = jH1;
|
||||
} else {
|
||||
jH1 = hneigh[j][0];
|
||||
jH2 = hneigh[j][1];
|
||||
if (hneigh[j][2] == 0) {
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
}
|
||||
}
|
||||
x2 = newsite[j];
|
||||
} else x2 = x[j];
|
||||
|
||||
delx = x1[0] - x2[0];
|
||||
dely = x1[1] - x2[1];
|
||||
delz = x1[2] - x2[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
// Coulombic interaction based on modified rsq
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r2inv = 1 / rsq;
|
||||
if (CTABLE || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
|
||||
cforce = forcecoul * r2inv;
|
||||
|
||||
// if i,j are not O atoms, force is applied directly
|
||||
// if i or j are O atoms, force is on fictitious atom & partitioned
|
||||
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
|
||||
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
|
||||
// preserves total force and torque on water molecule
|
||||
// virial = sum(r x F) where each water's atoms are near xi and xj
|
||||
// vlist stores 2,4,6 atoms whose forces contribute to virial
|
||||
|
||||
n = 0;
|
||||
|
||||
if (itype != typeO) {
|
||||
fxtmp += delx * cforce;
|
||||
fytmp += dely * cforce;
|
||||
fztmp += delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = x[i][0] * delx * cforce;
|
||||
v[1] = x[i][1] * dely * cforce;
|
||||
v[2] = x[i][2] * delz * cforce;
|
||||
v[3] = x[i][0] * dely * cforce;
|
||||
v[4] = x[i][0] * delz * cforce;
|
||||
v[5] = x[i][1] * delz * cforce;
|
||||
vlist[n++] = i;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = delx*cforce;
|
||||
fdy = dely*cforce;
|
||||
fdz = delz*cforce;
|
||||
|
||||
delxOM = x[i][0] - x1[0];
|
||||
delyOM = x[i][1] - x1[1];
|
||||
delzOM = x[i][2] - x1[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
fxtmp += fOx;
|
||||
fytmp += fOy;
|
||||
fztmp += fOz;
|
||||
|
||||
f[iH1][0] += fHx;
|
||||
f[iH1][1] += fHy;
|
||||
f[iH1][2] += fHz;
|
||||
|
||||
f[iH2][0] += fHx;
|
||||
f[iH2][1] += fHy;
|
||||
f[iH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[i],x[iH1],xH1);
|
||||
domain->closest_image(x[i],x[iH2],xH2);
|
||||
|
||||
v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = i;
|
||||
vlist[n++] = iH1;
|
||||
vlist[n++] = iH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (jtype != typeO) {
|
||||
f[j][0] -= delx * cforce;
|
||||
f[j][1] -= dely * cforce;
|
||||
f[j][2] -= delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] -= x[j][0] * delx * cforce;
|
||||
v[1] -= x[j][1] * dely * cforce;
|
||||
v[2] -= x[j][2] * delz * cforce;
|
||||
v[3] -= x[j][0] * dely * cforce;
|
||||
v[4] -= x[j][0] * delz * cforce;
|
||||
v[5] -= x[j][1] * delz * cforce;
|
||||
vlist[n++] = j;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = -delx*cforce;
|
||||
fdy = -dely*cforce;
|
||||
fdz = -delz*cforce;
|
||||
|
||||
delxOM = x[j][0] - x2[0];
|
||||
delyOM = x[j][1] - x2[1];
|
||||
delzOM = x[j][2] - x2[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
f[j][0] += fOx;
|
||||
f[j][1] += fOy;
|
||||
f[j][2] += fOz;
|
||||
|
||||
f[jH1][0] += fHx;
|
||||
f[jH1][1] += fHy;
|
||||
f[jH1][2] += fHz;
|
||||
|
||||
f[jH2][0] += fHx;
|
||||
f[jH2][1] += fHy;
|
||||
f[jH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[j],x[jH1],xH1);
|
||||
domain->closest_image(x[j],x[jH2],xH2);
|
||||
|
||||
v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = j;
|
||||
vlist[n++] = jH1;
|
||||
vlist[n++] = jH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (CTABLE || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongOMP::compute_newsite_thr(const double * xO,
|
||||
const double * xH1,
|
||||
const double * xH2,
|
||||
double * xM) const
|
||||
{
|
||||
double delx1 = xH1[0] - xO[0];
|
||||
double dely1 = xH1[1] - xO[1];
|
||||
double delz1 = xH1[2] - xO[2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2[0] - xO[0];
|
||||
double dely2 = xH2[1] - xO[1];
|
||||
double delz2 = xH2[2] - xO[2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
const double prefac = alpha * 0.5;
|
||||
xM[0] = xO[0] + prefac * (delx1 + delx2);
|
||||
xM[1] = xO[1] + prefac * (dely1 + dely2);
|
||||
xM[2] = xO[2] + prefac * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PLongOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutTIP4PLong::memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,51 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/tip4p/long/omp,PairLJCutTIP4PLongOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_TIP4P_LONG_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_TIP4P_LONG_OMP_H
|
||||
|
||||
#include "pair_lj_cut_tip4p_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTIP4PLongOMP : public PairLJCutTIP4PLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutTIP4PLongOMP(class LAMMPS *);
|
||||
virtual ~PairLJCutTIP4PLongOMP() {};
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int CFLAG, int EVFLAG, int EFLAG, int VFLAG>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
void compute_newsite_thr(const double *, const double *,
|
||||
const double *, double *) const;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,540 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_cut_tip4p_long_proxy_omp.h"
|
||||
#include "pppm_tip4p_proxy.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "update.h"
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutTIP4PLongProxyOMP::PairLJCutTIP4PLongProxyOMP(LAMMPS *lmp) :
|
||||
PairLJCutTIP4PLong(lmp), ThrOMP(lmp, THR_PAIR|THR_PROXY)
|
||||
{
|
||||
proxyflag = 1;
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
nproxy=1;
|
||||
|
||||
kspace = NULL;
|
||||
|
||||
// TIP4P cannot compute virial as F dot r
|
||||
// due to finding bonded H atoms which are not near O atom
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongProxyOMP::init_style()
|
||||
{
|
||||
if (comm->nthreads < 2)
|
||||
error->all(FLERR,"need at least two threads per MPI task for this pair style");
|
||||
|
||||
kspace = static_cast<PPPMTIP4PProxy *>(force->kspace);
|
||||
|
||||
PairLJCutTIP4PLong::init_style();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongProxyOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
const int nall = nlocal + atom->nghost;
|
||||
|
||||
// reallocate hneigh & newsite if necessary
|
||||
// initialize hneigh[0] to -1 on steps when reneighboring occurred
|
||||
// initialize hneigh[2] to 0 every step
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
nmax = atom->nmax;
|
||||
memory->destroy(hneigh);
|
||||
memory->create(hneigh,nmax,3,"pair:hneigh");
|
||||
memory->destroy(newsite);
|
||||
memory->create(newsite,nmax,3,"pair:newsite");
|
||||
}
|
||||
|
||||
// XXX: this could be threaded, too.
|
||||
int i;
|
||||
if (neighbor->ago == 0)
|
||||
for (i = 0; i < nall; i++) hneigh[i][0] = -1;
|
||||
for (i = 0; i < nall; i++) hneigh[i][2] = 0;
|
||||
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads, nproxy);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
// thread id 0 runs pppm, the rest the pair style
|
||||
if (tid < nproxy) {
|
||||
kspace->compute_proxy(eflag,vflag);
|
||||
} else {
|
||||
if (!ncoultablebits) {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<1,1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<1,1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<1,0,0,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag) eval<0,1,1,1>(ifrom, ito, thr);
|
||||
else eval<0,1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag) eval<0,1,0,1>(ifrom, ito, thr);
|
||||
else eval<0,1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<0,0,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
}
|
||||
|
||||
sync_threads();
|
||||
reduce_thr(this, eflag, vflag, thr, nproxy);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int CTABLE, int EVFLAG, int EFLAG, int VFLAG>
|
||||
void PairLJCutTIP4PLongProxyOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,ii,jj,jnum,itype,jtype,itable;
|
||||
int n,vlist[6];
|
||||
int iH1,iH2,jH1,jH2;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
|
||||
double fraction,table;
|
||||
double delxOM,delyOM,delzOM;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
|
||||
double factor_coul,factor_lj;
|
||||
double grij,expm2,prefactor,t,erfc,ddotf;
|
||||
double v[6],xH1[3],xH2[3];
|
||||
double fdx,fdy,fdz,f1x,f1y,f1z,fOx,fOy,fOz,fHx,fHy,fHz;
|
||||
const double *x1,*x2;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const int tid = thr->get_tid();
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
const double cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
|
||||
// if atom I = water O, set x1 = offset charge site
|
||||
// else x1 = x of atom I
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (itype == typeO) {
|
||||
if (hneigh[i][0] < 0) {
|
||||
iH1 = atom->map(atom->tag[i] + 1);
|
||||
iH2 = atom->map(atom->tag[i] + 2);
|
||||
if (iH1 == -1 || iH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
hneigh[i][1] = iH2;
|
||||
hneigh[i][0] = iH1;
|
||||
} else {
|
||||
iH1 = hneigh[i][0];
|
||||
iH2 = hneigh[i][1];
|
||||
if (hneigh[i][2] == 0) {
|
||||
compute_newsite_thr(x[i],x[iH1],x[iH2],newsite[i]);
|
||||
hneigh[i][2] = 1;
|
||||
}
|
||||
}
|
||||
x1 = newsite[i];
|
||||
} else x1 = x[i];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
// LJ interaction based on true rsq
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj * r2inv;
|
||||
|
||||
fxtmp += delx*forcelj;
|
||||
fytmp += dely*forcelj;
|
||||
fztmp += delz*forcelj;
|
||||
f[j][0] -= delx*forcelj;
|
||||
f[j][1] -= dely*forcelj;
|
||||
f[j][2] -= delz*forcelj;
|
||||
|
||||
if (EFLAG) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal, /* newton_pair = */ 1,
|
||||
evdwl,0.0,forcelj,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
// adjust rsq and delxyz for off-site O charge(s) if necessary
|
||||
// but only if they are within reach
|
||||
// NOTE: to make this part thread safe, we need to
|
||||
// make sure that the hneigh[][] entries only get
|
||||
// updated, when all data is in place. worst case,
|
||||
// some calculation is repeated, but since the results
|
||||
// will be the same, there is no race condition.
|
||||
if (rsq < cut_coulsqplus) {
|
||||
if (itype == typeO || jtype == typeO) {
|
||||
|
||||
// if atom J = water O, set x2 = offset charge site
|
||||
// else x2 = x of atom J
|
||||
|
||||
if (jtype == typeO) {
|
||||
if (hneigh[j][0] < 0) {
|
||||
jH1 = atom->map(atom->tag[j] + 1);
|
||||
jH2 = atom->map(atom->tag[j] + 2);
|
||||
if (jH1 == -1 || jH2 == -1)
|
||||
error->one(FLERR,"TIP4P hydrogen is missing");
|
||||
if (atom->type[jH1] != typeH || atom->type[jH2] != typeH)
|
||||
error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
hneigh[j][1] = jH2;
|
||||
hneigh[j][0] = jH1;
|
||||
} else {
|
||||
jH1 = hneigh[j][0];
|
||||
jH2 = hneigh[j][1];
|
||||
if (hneigh[j][2] == 0) {
|
||||
compute_newsite_thr(x[j],x[jH1],x[jH2],newsite[j]);
|
||||
hneigh[j][2] = 1;
|
||||
}
|
||||
}
|
||||
x2 = newsite[j];
|
||||
} else x2 = x[j];
|
||||
|
||||
delx = x1[0] - x2[0];
|
||||
dely = x1[1] - x2[1];
|
||||
delz = x1[2] - x2[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
}
|
||||
|
||||
// Coulombic interaction based on modified rsq
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r2inv = 1 / rsq;
|
||||
if (CTABLE || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) {
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
|
||||
cforce = forcecoul * r2inv;
|
||||
|
||||
// if i,j are not O atoms, force is applied directly
|
||||
// if i or j are O atoms, force is on fictitious atom & partitioned
|
||||
// force partitioning due to Feenstra, J Comp Chem, 20, 786 (1999)
|
||||
// f_f = fictitious force, fO = f_f (1 - 2 alpha), fH = alpha f_f
|
||||
// preserves total force and torque on water molecule
|
||||
// virial = sum(r x F) where each water's atoms are near xi and xj
|
||||
// vlist stores 2,4,6 atoms whose forces contribute to virial
|
||||
|
||||
n = 0;
|
||||
|
||||
if (itype != typeO) {
|
||||
fxtmp += delx * cforce;
|
||||
fytmp += dely * cforce;
|
||||
fztmp += delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = x[i][0] * delx * cforce;
|
||||
v[1] = x[i][1] * dely * cforce;
|
||||
v[2] = x[i][2] * delz * cforce;
|
||||
v[3] = x[i][0] * dely * cforce;
|
||||
v[4] = x[i][0] * delz * cforce;
|
||||
v[5] = x[i][1] * delz * cforce;
|
||||
vlist[n++] = i;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = delx*cforce;
|
||||
fdy = dely*cforce;
|
||||
fdz = delz*cforce;
|
||||
|
||||
delxOM = x[i][0] - x1[0];
|
||||
delyOM = x[i][1] - x1[1];
|
||||
delzOM = x[i][2] - x1[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
fxtmp += fOx;
|
||||
fytmp += fOy;
|
||||
fztmp += fOz;
|
||||
|
||||
f[iH1][0] += fHx;
|
||||
f[iH1][1] += fHy;
|
||||
f[iH1][2] += fHz;
|
||||
|
||||
f[iH2][0] += fHx;
|
||||
f[iH2][1] += fHy;
|
||||
f[iH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[i],x[iH1],xH1);
|
||||
domain->closest_image(x[i],x[iH2],xH2);
|
||||
|
||||
v[0] = x[i][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] = x[i][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] = x[i][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] = x[i][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] = x[i][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] = x[i][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = i;
|
||||
vlist[n++] = iH1;
|
||||
vlist[n++] = iH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (jtype != typeO) {
|
||||
f[j][0] -= delx * cforce;
|
||||
f[j][1] -= dely * cforce;
|
||||
f[j][2] -= delz * cforce;
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] -= x[j][0] * delx * cforce;
|
||||
v[1] -= x[j][1] * dely * cforce;
|
||||
v[2] -= x[j][2] * delz * cforce;
|
||||
v[3] -= x[j][0] * dely * cforce;
|
||||
v[4] -= x[j][0] * delz * cforce;
|
||||
v[5] -= x[j][1] * delz * cforce;
|
||||
vlist[n++] = j;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
fdx = -delx*cforce;
|
||||
fdy = -dely*cforce;
|
||||
fdz = -delz*cforce;
|
||||
|
||||
delxOM = x[j][0] - x2[0];
|
||||
delyOM = x[j][1] - x2[1];
|
||||
delzOM = x[j][2] - x2[2];
|
||||
|
||||
ddotf = (delxOM * fdx + delyOM * fdy + delzOM * fdz) /
|
||||
(qdist*qdist);
|
||||
|
||||
f1x = alpha * (fdx - ddotf * delxOM);
|
||||
f1y = alpha * (fdy - ddotf * delyOM);
|
||||
f1z = alpha * (fdz - ddotf * delzOM);
|
||||
|
||||
fOx = fdx - f1x;
|
||||
fOy = fdy - f1y;
|
||||
fOz = fdz - f1z;
|
||||
|
||||
fHx = 0.5 * f1x;
|
||||
fHy = 0.5 * f1y;
|
||||
fHz = 0.5 * f1z;
|
||||
|
||||
f[j][0] += fOx;
|
||||
f[j][1] += fOy;
|
||||
f[j][2] += fOz;
|
||||
|
||||
f[jH1][0] += fHx;
|
||||
f[jH1][1] += fHy;
|
||||
f[jH1][2] += fHz;
|
||||
|
||||
f[jH2][0] += fHx;
|
||||
f[jH2][1] += fHy;
|
||||
f[jH2][2] += fHz;
|
||||
|
||||
if (VFLAG) {
|
||||
domain->closest_image(x[j],x[jH1],xH1);
|
||||
domain->closest_image(x[j],x[jH2],xH2);
|
||||
|
||||
v[0] += x[j][0]*fOx + xH1[0]*fHx + xH2[0]*fHx;
|
||||
v[1] += x[j][1]*fOy + xH1[1]*fHy + xH2[1]*fHy;
|
||||
v[2] += x[j][2]*fOz + xH1[2]*fHz + xH2[2]*fHz;
|
||||
v[3] += x[j][0]*fOy + xH1[0]*fHy + xH2[0]*fHy;
|
||||
v[4] += x[j][0]*fOz + xH1[0]*fHz + xH2[0]*fHz;
|
||||
v[5] += x[j][1]*fOz + xH1[1]*fHz + xH2[1]*fHz;
|
||||
|
||||
vlist[n++] = j;
|
||||
vlist[n++] = jH1;
|
||||
vlist[n++] = jH2;
|
||||
}
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
if (CTABLE || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_list_thr(this,n,vlist,ecoul,v,thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
/* ----------------------------------------------------------------------
|
||||
compute position xM of fictitious charge site for O atom and 2 H atoms
|
||||
return it as xM
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutTIP4PLongProxyOMP::compute_newsite_thr(const double * xO,
|
||||
const double * xH1,
|
||||
const double * xH2,
|
||||
double * xM) const
|
||||
{
|
||||
double delx1 = xH1[0] - xO[0];
|
||||
double dely1 = xH1[1] - xO[1];
|
||||
double delz1 = xH1[2] - xO[2];
|
||||
domain->minimum_image(delx1,dely1,delz1);
|
||||
|
||||
double delx2 = xH2[0] - xO[0];
|
||||
double dely2 = xH2[1] - xO[1];
|
||||
double delz2 = xH2[2] - xO[2];
|
||||
domain->minimum_image(delx2,dely2,delz2);
|
||||
|
||||
const double prefac = alpha * 0.5;
|
||||
xM[0] = xO[0] + prefac * (delx1 + delx2);
|
||||
xM[1] = xO[1] + prefac * (dely1 + dely2);
|
||||
xM[2] = xO[2] + prefac * (delz1 + delz2);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutTIP4PLongProxyOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJCutTIP4PLong::memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/tip4p/long/proxy/omp,PairLJCutTIP4PLongProxyOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_TIP4P_LONG_PROXY_OMP_H
|
||||
#define LMP_PAIR_LJ_CUT_TIP4P_LONG_PROXY_OMP_H
|
||||
|
||||
#include "pair_lj_cut_tip4p_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutTIP4PLongProxyOMP :
|
||||
public PairLJCutTIP4PLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJCutTIP4PLongProxyOMP(class LAMMPS *);
|
||||
virtual ~PairLJCutTIP4PLongProxyOMP() {};
|
||||
|
||||
virtual void init_style();
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int, int, int, int>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
void compute_newsite_thr(const double *, const double *,
|
||||
const double *, double *) const;
|
||||
|
||||
class PPPMTIP4PProxy *kspace;
|
||||
int nproxy;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,233 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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_lj_long_coul_long_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "math_vector.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJLongCoulLongOMP::PairLJLongCoulLongOMP(LAMMPS *lmp) :
|
||||
PairLJLongCoulLong(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
cut_respa = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJLongCoulLongOMP::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 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
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairLJLongCoulLongOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
double evdwl,ecoul,fpair;
|
||||
evdwl = ecoul = 0.0;
|
||||
|
||||
const double * const * const x = atom->x;
|
||||
double * const * const f = thr->get_f();
|
||||
const double * const q = atom->q;
|
||||
const int * const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
const double * const special_coul = force->special_coul;
|
||||
const double * const special_lj = force->special_lj;
|
||||
const double qqrd2e = force->qqrd2e;
|
||||
|
||||
const double *x0 = x[0];
|
||||
double *f0 = f[0], *fi = f0;
|
||||
|
||||
int *ilist = list->ilist;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
int i, ii, j, order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6);
|
||||
int *jneigh, *jneighn, typei, typej, ni;
|
||||
double qi, qri, *cutsqi, *cut_ljsqi, *lj1i, *lj2i, *lj3i, *lj4i, *offseti;
|
||||
double rsq, r2inv, force_coul, force_lj;
|
||||
double g2 = g_ewald*g_ewald, g6 = g2*g2*g2, g8 = g6*g2;
|
||||
vector xi, d;
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) { // loop over my atoms
|
||||
i = ilist[ii]; fi = f0+3*i;
|
||||
if (order1) qri = (qi = q[i])*qqrd2e; // initialize constants
|
||||
offseti = offset[typei = type[i]];
|
||||
lj1i = lj1[typei]; lj2i = lj2[typei]; lj3i = lj3[typei]; lj4i = lj4[typei];
|
||||
cutsqi = cutsq[typei]; cut_ljsqi = cut_ljsq[typei];
|
||||
memcpy(xi, x0+(i+(i<<1)), sizeof(vector));
|
||||
jneighn = (jneigh = list->firstneigh[i])+list->numneigh[i];
|
||||
|
||||
for (; jneigh<jneighn; ++jneigh) { // loop over neighbors
|
||||
j = *jneigh;
|
||||
ni = sbmask(j);
|
||||
j &= NEIGHMASK;
|
||||
|
||||
{ register const double *xj = x0+(j+(j<<1));
|
||||
d[0] = xi[0] - xj[0]; // pair vector
|
||||
d[1] = xi[1] - xj[1];
|
||||
d[2] = xi[2] - xj[2]; }
|
||||
|
||||
if ((rsq = vec_dot(d, d)) >= cutsqi[typej = type[j]]) continue;
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (order1 && (rsq < cut_coulsq)) { // coulombic
|
||||
if (!ncoultablebits || rsq <= tabinnersq) { // series real space
|
||||
register double r = sqrt(rsq), x = g_ewald*r;
|
||||
register double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
|
||||
if (ni == 0) {
|
||||
s *= g_ewald*exp(-x*x);
|
||||
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
|
||||
if (EFLAG) ecoul = t;
|
||||
}
|
||||
else { // special case
|
||||
r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x);
|
||||
force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r;
|
||||
if (EFLAG) ecoul = t-r;
|
||||
}
|
||||
} // table real space
|
||||
else {
|
||||
register union_int_float_t t;
|
||||
t.f = rsq;
|
||||
register const int k = (t.i & ncoulmask)>>ncoulshiftbits;
|
||||
register double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
|
||||
if (ni == 0) {
|
||||
force_coul = qiqj*(ftable[k]+f*dftable[k]);
|
||||
if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]);
|
||||
}
|
||||
else { // special case
|
||||
t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
|
||||
force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
|
||||
if (EFLAG) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
|
||||
}
|
||||
}
|
||||
}
|
||||
else force_coul = ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsqi[typej]) { // lj
|
||||
if (order6) { // long-range lj
|
||||
register double rn = r2inv*r2inv*r2inv;
|
||||
register double x2 = g2*rsq, a2 = 1.0/x2;
|
||||
x2 = a2*exp(-x2)*lj4i[typej];
|
||||
if (ni == 0) {
|
||||
force_lj =
|
||||
(rn*=rn)*lj1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
|
||||
if (EFLAG)
|
||||
evdwl = rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2;
|
||||
}
|
||||
else { // special case
|
||||
register double f = special_lj[ni], t = rn*(1.0-f);
|
||||
force_lj = f*(rn *= rn)*lj1i[typej]-
|
||||
g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[typej];
|
||||
if (EFLAG)
|
||||
evdwl = f*rn*lj3i[typej]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[typej];
|
||||
}
|
||||
}
|
||||
else { // cut lj
|
||||
register double rn = r2inv*r2inv*r2inv;
|
||||
if (ni == 0) {
|
||||
force_lj = rn*(rn*lj1i[typej]-lj2i[typej]);
|
||||
if (EFLAG) evdwl = rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej];
|
||||
}
|
||||
else { // special case
|
||||
register double f = special_lj[ni];
|
||||
force_lj = f*rn*(rn*lj1i[typej]-lj2i[typej]);
|
||||
if (EFLAG)
|
||||
evdwl = f * (rn*(rn*lj3i[typej]-lj4i[typej])-offseti[typej]);
|
||||
}
|
||||
}
|
||||
}
|
||||
else force_lj = evdwl = 0.0;
|
||||
|
||||
fpair = (force_coul+force_lj)*r2inv;
|
||||
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
register double *fj = f0+(j+(j<<1)), f;
|
||||
fi[0] += f = d[0]*fpair; fj[0] -= f;
|
||||
fi[1] += f = d[1]*fpair; fj[1] -= f;
|
||||
fi[2] += f = d[2]*fpair; fj[2] -= f;
|
||||
}
|
||||
else {
|
||||
fi[0] += d[0]*fpair;
|
||||
fi[1] += d[1]*fpair;
|
||||
fi[2] += d[2]*fpair;
|
||||
}
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,NEWTON_PAIR,
|
||||
evdwl,ecoul,fpair,d[0],d[1],d[2],thr);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJLongCoulLongOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairLJLongCoulLong::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/long/coul/long/omp,PairLJLongCoulLongOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_LONG_COUL_LONG_OMP_H
|
||||
#define LMP_PAIR_LJ_LONG_COUL_LONG_OMP_H
|
||||
|
||||
#include "pair_lj_long_coul_long.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJLongCoulLongOMP : public PairLJLongCoulLong, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairLJLongCoulLongOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue