Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F87682596
pair_lj_cut_tip4p_long_opt.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Mon, Oct 14, 05:17
Size
14 KB
Mime Type
text/x-c
Expires
Wed, Oct 16, 05:17 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
21610271
Attached To
rLAMMPS lammps
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
Log In to Comment