Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
d3355b03dc0elammm-master

Last Change
Raw File

pair_lj_cut_coul_long_tip4p_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_coul_long_tip4p_opt.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "error.h"
#include "memory.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
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4POpt::PairLJCutCoulLongTIP4POpt(LAMMPS *lmp) :
PairLJCutCoulLongTIP4P(lmp)
{
single_enable = 0;
respa_enable = 0;
// TIP4P cannot compute virial as F dot r
// due to find_M() finding bonded H atoms which are not near O atom
no_virial_fdotr_compute = 1;
// for caching m-shift corrected positions
maxmpos = 0;
h1idx = h2idx = NULL;
mpos = NULL;
}
PairLJCutCoulLongTIP4POpt::~PairLJCutCoulLongTIP4POpt()
{
memory->destroy(h1idx);
memory->destroy(h2idx);
memory->destroy(mpos);
}
void PairLJCutCoulLongTIP4POpt::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 per-atom arrays, if necessary
if (nall > maxmpos) {
maxmpos = nall;
memory->grow(mpos,maxmpos,3,"pair:mpos");
memory->grow(h1idx,maxmpos,"pair:h1idx");
memory->grow(h2idx,maxmpos,"pair:h2idx");
}
// cache corrected M positions in mpos[]
double **x = atom->x;
int *type = atom->type;
for (int i = 0; i < nlocal; i++) {
if (type[i] == typeO) {
find_M(i,h1idx[i],h2idx[i],mpos[i]);
} else {
mpos[i][0] = x[i][0];
mpos[i][1] = x[i][1];
mpos[i][2] = x[i][2];
}
}
for (int i = nlocal; i < nall; i++) {
if (type[i] == typeO) {
find_M_permissive(i,h1idx[i],h2idx[i],mpos[i]);
} else {
mpos[i][0] = x[i][0];
mpos[i][1] = x[i][1];
mpos[i][2] = x[i][2];
}
}
if (!ncoultablebits) {
if (evflag) {
if (eflag) {
if (vflag) {
if (force->newton_pair) return eval<1,1,1,1,0>();
else return eval<1,1,1,0,0>();
} else {
if (force->newton_pair) return eval<1,1,0,1,0>();
else return eval<1,1,0,0,0>();
}
} else {
if (vflag) {
if (force->newton_pair) return eval<1,0,1,1,0>();
else return eval<1,0,1,0,0>();
} else {
if (force->newton_pair) return eval<1,0,0,1,0>();
else return eval<1,0,0,0,0>();
}
}
} else {
if (force->newton_pair) return eval<0,0,0,1,0>();
else return eval<0,0,0,0,0>();
}
} else {
if (evflag) {
if (eflag) {
if (vflag) {
if (force->newton_pair) return eval<1,1,1,1,1>();
else return eval<1,1,1,0,1>();
} else {
if (force->newton_pair) return eval<1,1,0,1,1>();
else return eval<1,1,0,0,1>();
}
} else {
if (vflag) {
if (force->newton_pair) return eval<1,0,1,1,1>();
else return eval<1,0,1,0,1>();
} else {
if (force->newton_pair) return eval<1,0,0,1,1>();
else return eval<1,0,0,0,1>();
}
}
} else {
if (force->newton_pair) return eval<0,0,0,1,1>();
else return eval<0,0,0,0,1>();
}
}
}
/* ---------------------------------------------------------------------- */
template < const int EVFLAG, const int EFLAG, const int VFLAG,
const int NEWTON_PAIR, const int CTABLE >
void PairLJCutCoulLongTIP4POpt::eval()
{
int i,j,ii,jj,inum,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,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;
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
evdwl = ecoul = 0.0;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
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];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=0.0;
x1 = mpos[i];
iH1 = h1idx[i];
iH2 = h2idx[i];
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_ljsq[itype][jtype]) {
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,
evdwl,0.0,forcelj,delx,dely,delz);
}
// adjust rsq and delxyz for off-site O charge(s)
if (itype == typeO || jtype == typeO) {
x2 = mpos[j];
jH1 = h1idx[j];
jH2 = h2idx[j];
if (jtype == typeO && ( jH1 < 0 || jH2 < 0))
error->one(FLERR,"TIP4P hydrogen is missing");
delx = x1[0] - x2[0];
dely = x1[1] - x2[1];
delz = x1[2] - x2[2];
rsq = delx*delx + dely*dely + delz*delz;
}
// test current rsq against cutoff and compute Coulombic force
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(n,vlist,ecoul,v);
}
}
}
f[i][0] += fxtmp;
f[i][1] += fytmp;
f[i][2] += fztmp;
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4POpt::find_M_permissive(int i, int &iH1, int &iH2, double *xM)
{
// test that O is correctly bonded to 2 succesive H atoms
iH1 = atom->map(atom->tag[i] + 1);
iH2 = atom->map(atom->tag[i] + 2);
if (iH1 == -1 || iH2 == -1)
return;
else
find_M(i,iH1,iH2,xM);
}
/* ---------------------------------------------------------------------- */
double PairLJCutCoulLongTIP4POpt::memory_usage()
{
double bytes = PairLJCutCoulLongTIP4P::memory_usage();
bytes += 2 * maxmpos * sizeof(int);
bytes += 3 * maxmpos * sizeof(double);
bytes += maxmpos * sizeof(double *);
return bytes;
}
c4science · Help