-
sjplimp authored
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7873 f3b2605a-c512-4ea7-a41b-209d697bcdaa
sjplimp authoredgit-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7873 f3b2605a-c512-4ea7-a41b-209d697bcdaa
pair_lj_cut_coul_long_tip4p.cpp 15.36 KiB
/* ----------------------------------------------------------------------
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 authors: Amalie Frischknecht and Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_coul_long_tip4p.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.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
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
PairLJCutCoulLong(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;
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::compute(int eflag, int vflag)
{
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 xiM[3],xjM[3],fO[3],fH[3],fd[3],f1[3],v[6],xH1[3],xH2[3];
double *x1,*x2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 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 cut_coulsqplus = (cut_coul+2.0*qdist) * (cut_coul+2.0*qdist);
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 (itype == typeO) {
find_M(i,iH1,iH2,xiM);
x1 = xiM;
} else x1 = x[i];
jlist = firstneigh[i];
jnum = numneigh[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];
// 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;
f[i][0] += delx*forcelj;
f[i][1] += dely*forcelj;
f[i][2] += 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 necessary
// but only if they are within reach
if (rsq < cut_coulsqplus) {
if (itype == typeO || jtype == typeO) {
if (jtype == typeO) {
find_M(j,jH1,jH2,xjM);
x2 = xjM;
} 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 (!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;
}
}
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) {
f[i][0] += delx * cforce;
f[i][1] += dely * cforce;
f[i][2] += 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 {
fd[0] = delx*cforce;
fd[1] = dely*cforce;
fd[2] = delz*cforce;
delxOM = x[i][0] - x1[0];
delyOM = x[i][1] - x1[1];
delzOM = x[i][2] - x1[2];
ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
(qdist*qdist);
f1[0] = ddotf * delxOM;
f1[1] = ddotf * delyOM;
f1[2] = ddotf * delzOM;
fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
f[i][0] += fO[0];
f[i][1] += fO[1];
f[i][2] += fO[2];
f[iH1][0] += fH[0];
f[iH1][1] += fH[1];
f[iH1][2] += fH[2];
f[iH2][0] += fH[0];
f[iH2][1] += fH[1];
f[iH2][2] += fH[2];
if (vflag) {
domain->closest_image(x[i],x[iH1],xH1);
domain->closest_image(x[i],x[iH2],xH2);
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
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 {
fd[0] = -delx*cforce;
fd[1] = -dely*cforce;
fd[2] = -delz*cforce;
delxOM = x[j][0] - x2[0];
delyOM = x[j][1] - x2[1];
delzOM = x[j][2] - x2[2];
ddotf = (delxOM * fd[0] + delyOM * fd[1] + delzOM * fd[2]) /
(qdist*qdist);
f1[0] = ddotf * delxOM;
f1[1] = ddotf * delyOM;
f1[2] = ddotf * delzOM;
fO[0] = fd[0] - alpha * (fd[0] - f1[0]);
fO[1] = fd[1] - alpha * (fd[1] - f1[1]);
fO[2] = fd[2] - alpha * (fd[2] - f1[2]);
fH[0] = 0.5 * alpha * (fd[0] - f1[0]);
fH[1] = 0.5 * alpha * (fd[1] - f1[1]);
fH[2] = 0.5 * alpha * (fd[2] - f1[2]);
f[j][0] += fO[0];
f[j][1] += fO[1];
f[j][2] += fO[2];
f[jH1][0] += fH[0];
f[jH1][1] += fH[1];
f[jH1][2] += fH[2];
f[jH2][0] += fH[0];
f[jH2][1] += fH[1];
f[jH2][2] += fH[2];
if (vflag) {
domain->closest_image(x[j],x[jH1],xH1);
domain->closest_image(x[j],x[jH2],xH2);
v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
vlist[n++] = j;
vlist[n++] = jH1;
vlist[n++] = jH2;
}
}
if (eflag) {
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 (evflag) ev_tally_list(n,vlist,ecoul,v);
}
}
}
}
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::settings(int narg, char **arg)
{
if (narg < 6 || narg > 7) error->all(FLERR,"Illegal pair_style command");
typeO = force->inumeric(arg[0]);
typeH = force->inumeric(arg[1]);
typeB = force->inumeric(arg[2]);
typeA = force->inumeric(arg[3]);
qdist = force->numeric(arg[4]);
cut_lj_global = force->numeric(arg[5]);
if (narg == 6) cut_coul = cut_lj_global;
else cut_coul = force->numeric(arg[6]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style lj/cut/coul/long/tip4p requires atom IDs");
if (!force->newton_pair)
error->all(FLERR,
"Pair style lj/cut/coul/long/tip4p requires newton pair on");
if (!atom->q_flag)
error->all(FLERR,
"Pair style lj/cut/coul/long/tip4p requires atom attribute q");
if ( (strcmp(force->kspace_style,"pppm/tip4p") != 0) &&
(strcmp(force->kspace_style,"pppm/tip4p/omp") != 0) &&
(strcmp(force->kspace_style,"pppm/tip4p/proxy") != 0) )
error->all(FLERR,"Pair style is incompatible with KSpace style");
if (force->bond == NULL)
error->all(FLERR,"Must use a bond style with TIP4P potential");
if (force->angle == NULL)
error->all(FLERR,"Must use an angle style with TIP4P potential");
PairLJCutCoulLong::init_style();
// set alpha parameter
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (cos(0.5*theta) * blen);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::write_restart_settings(FILE *fp)
{
fwrite(&typeO,sizeof(int),1,fp);
fwrite(&typeH,sizeof(int),1,fp);
fwrite(&typeB,sizeof(int),1,fp);
fwrite(&typeA,sizeof(int),1,fp);
fwrite(&qdist,sizeof(double),1,fp);
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&typeO,sizeof(int),1,fp);
fread(&typeH,sizeof(int),1,fp);
fread(&typeB,sizeof(int),1,fp);
fread(&typeA,sizeof(int),1,fp);
fread(&qdist,sizeof(double),1,fp);
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&typeO,1,MPI_INT,0,world);
MPI_Bcast(&typeH,1,MPI_INT,0,world);
MPI_Bcast(&typeB,1,MPI_INT,0,world);
MPI_Bcast(&typeA,1,MPI_INT,0,world);
MPI_Bcast(&qdist,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
find 2 H atoms bonded to O atom i
compute position xM of fictitious charge site for O atom
also return local indices iH1,iH2 of H atoms
------------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::find_M(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) 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");
double **x = atom->x;
double delx1 = x[iH1][0] - x[i][0];
double dely1 = x[iH1][1] - x[i][1];
double delz1 = x[iH1][2] - x[i][2];
domain->minimum_image(delx1,dely1,delz1);
double delx2 = x[iH2][0] - x[i][0];
double dely2 = x[iH2][1] - x[i][1];
double delz2 = x[iH2][2] - x[i][2];
domain->minimum_image(delx2,dely2,delz2);
xM[0] = x[i][0] + alpha * 0.5 * (delx1 + delx2);
xM[1] = x[i][1] + alpha * 0.5 * (dely1 + dely2);
xM[2] = x[i][2] + alpha * 0.5 * (delz1 + delz2);
}
/* ---------------------------------------------------------------------- */
void *PairLJCutCoulLongTIP4P::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"qdist") == 0) return (void *) &qdist;
if (strcmp(str,"typeO") == 0) return (void *) &typeO;
if (strcmp(str,"typeH") == 0) return (void *) &typeH;
if (strcmp(str,"typeA") == 0) return (void *) &typeA;
if (strcmp(str,"typeB") == 0) return (void *) &typeB;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
return NULL;
}