Page MenuHomec4science
Files F71389620

pair_lj_cut_tip4p_long_opt.cpp
No OneTemporary
Actions

File Metadata

Created
Thu, Jul 11, 11:18

pair_lj_cut_tip4p_long_opt.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
OPT version: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_lj_cut_tip4p_long_opt.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "error.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.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
/* ---------------------------------------------------------------------- */
PairLJCutTIP4PLongOpt::PairLJCutTIP4PLongOpt(LAMMPS *lmp) :
PairLJCutTIP4PLong(lmp)
{
single_enable = 0;
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 PairLJCutTIP4PLongOpt::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");
}
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;
if (!ncoultablebits) {
if (evflag) {
if (eflag) {
if (vflag) return eval<1,1,1,1>();
else return eval<1,1,1,0>();
} else {
if (vflag) return eval<1,1,0,1>();
else return eval<1,1,0,0>();
}
} else return eval<1,0,0,0>();
} else {
if (evflag) {
if (eflag) {
if (vflag) return eval<0,1,1,1>();
else return eval<0,1,1,0>();
} else {
if (vflag) return eval<0,1,0,1>();
else return eval<0,1,0,0>();
}
} else return eval<0,0,0,0>();
}
}
/* ---------------------------------------------------------------------- */
template < const int CTABLE, const int EVFLAG,
const int EFLAG, const int VFLAG>
void PairLJCutTIP4PLongOpt::eval()
{
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double fraction,table;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double v[6],xH1[3],xH2[3];
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
const double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
int i,j,ii,jj,inum,jnum,itype,jtype,itable,key;
int n,vlist[6];
int iH1,iH2,jH1,jH2;
evdwl = ecoul = 0.0;
const double * const * const x = atom->x;
double * const * const f = atom->f;
const double * const q = atom->q;
const tagint * const tag = atom->tag;
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 cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
double fxtmp,fytmp,fztmp;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; 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
if (itype == typeO) {
if (hneigh[i][0] < 0) {
hneigh[i][0] = iH1 = atom->map(tag[i] + 1);
hneigh[i][1] = iH2 = atom->map(tag[i] + 2);
hneigh[i][2] = 1;
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_opt(x[i],x[iH1],x[iH2],newsite[i]);
} else {
iH1 = hneigh[i][0];
iH2 = hneigh[i][1];
if (hneigh[i][2] == 0) {
hneigh[i][2] = 1;
compute_newsite_opt(x[i],x[iH1],x[iH2],newsite[i]);
}
}
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(i,j,nlocal,/* newton_pair = */ 1,
evdwl,0.0,forcelj,delx,dely,delz);
}
// adjust rsq and delxyz for off-site O charge(s) if necessary
// but only if they are within reach
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) {
hneigh[j][0] = jH1 = atom->map(tag[j] + 1);
hneigh[j][1] = jH2 = atom->map(tag[j] + 2);
hneigh[j][2] = 1;
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_opt(x[j],x[jH1],x[jH2],newsite[j]);
} else {
jH1 = hneigh[j][0];
jH2 = hneigh[j][1];
if (hneigh[j][2] == 0) {
hneigh[j][2] = 1;
compute_newsite_opt(x[j],x[jH1],x[jH2],newsite[j]);
}
}
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
if (EVFLAG) {
n = 0;
key = 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;
}
if (EVFLAG) vlist[n++] = i;
} else {
if (EVFLAG) key += 1;
fdx = delx*cforce;
fdy = dely*cforce;
fdz = delz*cforce;
fOx = fdx*(1-alpha);
fOy = fdy*(1-alpha);
fOz = fdz*(1-alpha);
fHx = 0.5 * alpha * fdx;
fHy = 0.5 * alpha * fdy;
fHz = 0.5 * alpha * fdz;
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;
}
if (EVFLAG) {
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;
}
if (EVFLAG) vlist[n++] = j;
} else {
if (EVFLAG) key += 2;
fdx = -delx*cforce;
fdy = -dely*cforce;
fdz = -delz*cforce;
fOx = fdx*(1-alpha);
fOy = fdy*(1-alpha);
fOz = fdz*(1-alpha);
fHx = 0.5 * alpha * fdx;
fHy = 0.5 * alpha * fdy;
fHz = 0.5 * alpha * fdz;
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;
}
if (EVFLAG) {
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_tip4p(key,vlist,v,ecoul,alpha);
}
}
}
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 PairLJCutTIP4PLongOpt::compute_newsite_opt(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 PairLJCutTIP4PLongOpt::memory_usage()
{
double bytes = PairLJCutTIP4PLong::memory_usage();
return bytes;
}

Event Timeline

c4science · Help