/* ---------------------------------------------------------------------- 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) Rolf Isele-Holder (Aachen University) ------------------------------------------------------------------------- */ #include "pair_lj_long_tip4p_long.h" #include #include #include #include "angle.h" #include "atom.h" #include "bond.h" #include "comm.h" #include "domain.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" #include "utils.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 /* ---------------------------------------------------------------------- */ PairLJLongTIP4PLong::PairLJLongTIP4PLong(LAMMPS *lmp) : PairLJLongCoulLong(lmp) { dispersionflag = tip4pflag = 1; single_enable = 0; respa_enable = 1; nmax = 0; hneigh = NULL; newsite = NULL; // 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; } /* ---------------------------------------------------------------------- */ PairLJLongTIP4PLong::~PairLJLongTIP4PLong() { memory->destroy(hneigh); memory->destroy(newsite); } /* ---------------------------------------------------------------------- */ void PairLJLongTIP4PLong::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype,itable; int n,vlist[6]; int key; int iH1,iH2,jH1,jH2; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul; double fraction,table; double r,r2inv,forcecoul,forcelj,cforce; double factor_coul; double grij,expm2,prefactor,t,erfc; double fO[3],fH[3],fd[3],v[6]; double *x1,*x2,*xH1,*xH2; int *ilist,*jlist,*numneigh,**firstneigh; double rsq; evdwl = ecoul = 0.0; ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred // initialize hneigh[2] to 0 every step int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; 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"); } if (neighbor->ago == 0) for (i = 0; i < nall; i++) hneigh[i][0] = -1; for (i = 0; i < nall; i++) hneigh[i][2] = 0; double **f = atom->f; double **x = atom->x; double *q = atom->q; tagint *tag = atom->tag; int *type = atom->type; 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); int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6); int ni; double *lj1i, *lj2i, *lj3i, *lj4i, *offseti; double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2; 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) { if (hneigh[i][0] < 0) { iH1 = atom->map(tag[i] + 1); iH2 = atom->map(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"); // set iH1,iH2 to closest image to O iH1 = domain->closest_image(i,iH1); iH2 = domain->closest_image(i,iH2); compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); hneigh[i][0] = iH1; hneigh[i][1] = iH2; hneigh[i][2] = 1; } else { iH1 = hneigh[i][0]; iH2 = hneigh[i][1]; if (hneigh[i][2] == 0) { hneigh[i][2] = 1; compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); } } x1 = newsite[i]; } else x1 = x[i]; jlist = firstneigh[i]; jnum = numneigh[i]; offseti = offset[itype]; lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; ni = 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 < cut_ljsq[itype][jtype]) { // lj r2inv = 1.0/rsq; if (order6) { // long-range lj if (!ndisptablebits || rsq <= tabinnerdispsq) { double rn = r2inv*r2inv*r2inv; double x2 = g2*rsq, a2 = 1.0/x2; x2 = a2*exp(-x2)*lj4i[jtype]; if (ni == 0) { forcelj = (rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq; if (eflag) evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2; } else { // special case double f = special_lj[ni], t = rn*(1.0-f); forcelj = f*(rn *= rn)*lj1i[jtype]- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype]; if (eflag) evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype]; } } else { // table real space union_int_float_t disp_t; disp_t.f = rsq; const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits; double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k]; double rn = r2inv*r2inv*r2inv; if (ni == 0) { forcelj = (rn*=rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]; if (eflag) evdwl = rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]; } else { // special case double f = special_lj[ni], t = rn*(1.0-f); forcelj = f*(rn *= rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]+t*lj2i[jtype]; if (eflag) evdwl = f*rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]+t*lj4i[jtype]; } } } else { // cut lj double rn = r2inv*r2inv*r2inv; if (ni == 0) { forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]); if (eflag) evdwl = rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype]; } else { // special case double f = special_lj[ni]; forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype]); if (eflag) evdwl = f * (rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype]); } } forcelj *= 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 (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) // ADDITIONAL REQEUST REQUIRED HERE!!!!! if (rsq < cut_coulsqplus) { if (itype == typeO || jtype == typeO) { if (jtype == typeO) { if (hneigh[j][0] < 0) { jH1 = atom->map(tag[j] + 1); jH2 = atom->map(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"); // set jH1,jH2 to closest image to O jH1 = domain->closest_image(j,jH1); jH2 = domain->closest_image(j,jH2); compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); hneigh[j][0] = jH1; hneigh[j][1] = jH2; hneigh[j][2] = 1; } else { jH1 = hneigh[j][0]; jH2 = hneigh[j][1]; if (hneigh[j][2] == 0) { hneigh[j][2] = 1; compute_newsite(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; } // test current rsq against cutoff and compute Coulombic force if (rsq < cut_coulsq && order1) { r2inv = 1.0 / 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 (evflag) ev_tally(i,j,nlocal,newton_pair, // evdwl,0.0,cforce,delx,dely,delz); // 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; key = 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 { key += 1; fd[0] = delx*cforce; fd[1] = dely*cforce; fd[2] = delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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) { xH1 = x[iH1]; xH2 = x[iH2]; 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 { key += 2; fd[0] = -delx*cforce; fd[1] = -dely*cforce; fd[2] = -delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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) { xH1 = x[jH1]; xH2 = x[jH2]; 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_tip4p(key,vlist,v,ecoul,alpha); } } } } } /* --------------------------------------------------------------------- */ void PairLJLongTIP4PLong::compute_inner() { int i,j,ii,jj,inum,jnum,itype,jtype; int iH1,iH2,jH1,jH2; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz; double r2inv,forcecoul,forcelj,cforce; double fO[3],fH[3],fd[3]; double *x1,*x2; int *ilist,*jlist,*numneigh,**firstneigh; double rsq, qri; double cut_out_on = cut_respa[0]; double cut_out_off = cut_respa[1]; double cut_out_diff = cut_out_off - cut_out_on; double cut_out_on_sq = cut_out_on*cut_out_on; double cut_out_off_sq = cut_out_off*cut_out_off; // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred // initialize hneigh[2] to 0 every step int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; // atom->nmax > nmax will occur during setup 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"); } if (neighbor->ago == 0) for (i = 0; i < nall; i++) hneigh[i][0] = -1; for (i = 0; i < nall; i++) hneigh[i][2] = 0; double **f = atom->f; double **x = atom->x; double *q = atom->q; tagint *tag = atom->tag; int *type = atom->type; double *special_coul = force->special_coul; double *special_lj = force->special_lj; double qqrd2e = force->qqrd2e; double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist); int order1 = ewald_order&(1<<1); int ni; double *lj1i, *lj2i; inum = list->inum_inner; ilist = list->ilist_inner; numneigh = list->numneigh_inner; firstneigh = list->firstneigh_inner; // 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 && order1) { if (hneigh[i][0] < 0) { iH1 = atom->map(tag[i] + 1); iH2 = atom->map(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"); // set iH1,iH2 to closest image to O iH1 = domain->closest_image(i,iH1); iH2 = domain->closest_image(i,iH2); compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); hneigh[i][0] = iH1; hneigh[i][1] = iH2; hneigh[i][2] = 1; } else { iH1 = hneigh[i][0]; iH2 = hneigh[i][1]; if (hneigh[i][2] == 0) { hneigh[i][2] = 1; compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); } } x1 = newsite[i]; } else x1 = x[i]; jlist = firstneigh[i]; jnum = numneigh[i]; lj1i = lj1[itype]; lj2i = lj2[itype]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; ni = 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 < cut_ljsq[itype][jtype] && rsq < cut_out_off_sq ) { // lj r2inv = 1.0/rsq; double rn = r2inv*r2inv*r2inv; if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]); else { // special case double f = special_lj[ni]; forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype]); } if (rsq > cut_out_on_sq) { // switching double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; forcelj *= 1.0 + rsw*rsw*(2.0*rsw-3.0); } forcelj *= 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; } // adjust rsq and delxyz for off-site O charge(s) // ADDITIONAL REQEUST REQUIRED HERE!!!!! if (rsq < cut_coulsqplus && order1) { if (itype == typeO || jtype == typeO) { if (jtype == typeO) { if (hneigh[j][0] < 0) { jH1 = atom->map(tag[j] + 1); jH2 = atom->map(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"); // set jH1,jH2 to closest image to O jH1 = domain->closest_image(j,jH1); jH2 = domain->closest_image(j,jH2); compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); hneigh[j][0] = jH1; hneigh[j][1] = jH2; hneigh[j][2] = 1; } else { jH1 = hneigh[j][0]; jH2 = hneigh[j][1]; if (hneigh[j][2] == 0) { hneigh[j][2] = 1; compute_newsite(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; } // test current rsq against cutoff and compute Coulombic force if (rsq < cut_coulsq && rsq < cut_out_off_sq) { r2inv = 1.0 / rsq; qri = qqrd2e*qtmp; if (ni == 0) forcecoul = qri*q[j]*sqrt(r2inv); else { forcecoul = qri*q[j]*sqrt(r2inv)*special_coul[ni]; } if (rsq > cut_out_on_sq) { // switching double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; forcecoul *= 1.0 + rsw*rsw*(2.0*rsw-3.0); } cforce = forcecoul * r2inv; //if (evflag) ev_tally(i,j,nlocal,newton_pair, // evdwl,0.0,cforce,delx,dely,delz); // 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 (itype != typeO) { f[i][0] += delx * cforce; f[i][1] += dely * cforce; f[i][2] += delz * cforce; } else { fd[0] = delx*cforce; fd[1] = dely*cforce; fd[2] = delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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 (jtype != typeO) { f[j][0] -= delx * cforce; f[j][1] -= dely * cforce; f[j][2] -= delz * cforce; } else { fd[0] = -delx*cforce; fd[1] = -dely*cforce; fd[2] = -delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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]; } } } } } } /* --------------------------------------------------------------------- */ void PairLJLongTIP4PLong::compute_middle() { int i,j,ii,jj,inum,jnum,itype,jtype; int iH1,iH2,jH1,jH2; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz; double r2inv,forcecoul,forcelj,cforce; double fO[3],fH[3],fd[3]; double *x1,*x2; int *ilist,*jlist,*numneigh,**firstneigh; double rsq,qri; double cut_in_off = cut_respa[0]; double cut_in_on = cut_respa[1]; double cut_out_on = cut_respa[2]; double cut_out_off = cut_respa[3]; double cut_in_diff = cut_in_on - cut_in_off; double cut_out_diff = cut_out_off - cut_out_on; double cut_in_off_sq = cut_in_off*cut_in_off; double cut_in_on_sq = cut_in_on*cut_in_on; double cut_out_on_sq = cut_out_on*cut_out_on; double cut_out_off_sq = cut_out_off*cut_out_off; // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred // initialize hneigh[2] to 0 every step double **f = atom->f; double **x = atom->x; double *q = atom->q; tagint *tag = atom->tag; int *type = atom->type; double *special_coul = force->special_coul; double *special_lj = force->special_lj; double qqrd2e = force->qqrd2e; double cut_coulsqplus = (cut_coul+2.0*qdist)*(cut_coul+2.0*qdist); int order1 = ewald_order&(1<<1); int ni; double *lj1i, *lj2i; inum = list->inum_middle; ilist = list->ilist_middle; numneigh = list->numneigh_middle; firstneigh = list->firstneigh_middle; // 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 && order1) { if (hneigh[i][0] < 0) { iH1 = atom->map(tag[i] + 1); iH2 = atom->map(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"); // set iH1,iH2 to closest image to O iH1 = domain->closest_image(i,iH1); iH2 = domain->closest_image(i,iH2); compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); hneigh[i][0] = iH1; hneigh[i][1] = iH2; hneigh[i][2] = 1; } else { iH1 = hneigh[i][0]; iH2 = hneigh[i][1]; if (hneigh[i][2] == 0) { hneigh[i][2] = 1; compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); } } x1 = newsite[i]; } else x1 = x[i]; jlist = firstneigh[i]; jnum = numneigh[i]; lj1i = lj1[itype]; lj2i = lj2[itype]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; ni = 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 < cut_ljsq[itype][jtype] && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq ) { // lj r2inv = 1.0/rsq; double rn = r2inv*r2inv*r2inv; if (ni == 0) forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype]); else { // special case double f = special_lj[ni]; forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype]); } if (rsq < cut_in_on_sq) { // switching double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; forcelj *= rsw*rsw*(3.0 - 2.0*rsw); } if (rsq > cut_out_on_sq) { double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; forcelj *= 1.0 + rsw*rsw*(2.0*rsw-3.0); } forcelj *= 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; } // adjust rsq and delxyz for off-site O charge(s) // ADDITIONAL REQEUST REQUIRED HERE!!!!! if (rsq < cut_coulsqplus && order1) { if (itype == typeO || jtype == typeO) { if (jtype == typeO) { if (hneigh[j][0] < 0) { jH1 = atom->map(tag[j] + 1); jH2 = atom->map(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"); // set jH1,jH2 to closest image to O jH1 = domain->closest_image(j,jH1); jH2 = domain->closest_image(j,jH2); compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); hneigh[j][0] = jH1; hneigh[j][1] = jH2; hneigh[j][2] = 1; } else { jH1 = hneigh[j][0]; jH2 = hneigh[j][1]; if (hneigh[j][2] == 0) { hneigh[j][2] = 1; compute_newsite(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; } // test current rsq against cutoff and compute Coulombic force if (rsq < cut_coulsq && rsq >= cut_in_off_sq && rsq <= cut_out_off_sq) { r2inv = 1.0 / rsq; qri = qqrd2e*qtmp; if (ni == 0) forcecoul = qri*q[j]*sqrt(r2inv); else { forcecoul = qri*q[j]*sqrt(r2inv)*special_coul[ni]; } if (rsq < cut_in_on_sq) { // switching double rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; forcecoul *= rsw*rsw*(3.0 - 2.0*rsw); } if (rsq > cut_out_on_sq) { double rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; forcecoul *= 1.0 + rsw*rsw*(2.0*rsw-3.0); } cforce = forcecoul * r2inv; //if (evflag) ev_tally(i,j,nlocal,newton_pair, // evdwl,0.0,cforce,delx,dely,delz); // 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 (itype != typeO) { f[i][0] += delx * cforce; f[i][1] += dely * cforce; f[i][2] += delz * cforce; } else { fd[0] = delx*cforce; fd[1] = dely*cforce; fd[2] = delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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 (jtype != typeO) { f[j][0] -= delx * cforce; f[j][1] -= dely * cforce; f[j][2] -= delz * cforce; } else { fd[0] = -delx*cforce; fd[1] = -dely*cforce; fd[2] = -delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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]; } } } } } } /* --------------------------------------------------------------------- */ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; int n,vlist[6]; int key; int iH1,iH2,jH1,jH2; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul; double r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa,fvirial; double fO[3],fH[3],fd[3],v[6]; double *x1,*x2,*xH1,*xH2; int *ilist,*jlist,*numneigh,**firstneigh; double rsq,qri; int respa_flag; evdwl = ecoul = 0.0; ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred // initialize hneigh[2] to 0 every step int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; 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"); } if (neighbor->ago == 0) { for (i = 0; i < nall; i++) hneigh[i][0] = -1; for (i = 0; i < nall; i++) hneigh[i][2] = 0; } double **f = atom->f; double **x = atom->x; double *q = atom->q; tagint *tag = atom->tag; int *type = atom->type; 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); int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6); int ni; double *lj1i, *lj2i, *lj3i, *lj4i, *offseti; double g2 = g_ewald_6*g_ewald_6, g6 = g2*g2*g2, g8 = g6*g2; double cut_in_off = cut_respa[2]; double cut_in_on = cut_respa[3]; double cut_in_diff = cut_in_on - cut_in_off; double cut_in_off_sq = cut_in_off*cut_in_off; double cut_in_on_sq = cut_in_on*cut_in_on; 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]; qri = qtmp*qqrd2e; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; if (itype == typeO) { if (hneigh[i][0] < 0) { iH1 = atom->map(tag[i] + 1); iH2 = atom->map(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"); // set iH1,iH2 to closest image to O iH1 = domain->closest_image(i,iH1); iH2 = domain->closest_image(i,iH2); compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); hneigh[i][0] = iH1; hneigh[i][1] = iH2; hneigh[i][2] = 1; } else { iH1 = hneigh[i][0]; iH2 = hneigh[i][1]; if (hneigh[i][2] == 0) { hneigh[i][2] = 1; compute_newsite(x[i],x[iH1],x[iH2],newsite[i]); } } x1 = newsite[i]; } else x1 = x[i]; jlist = firstneigh[i]; jnum = numneigh[i]; offseti = offset[itype]; lj1i = lj1[itype]; lj2i = lj2[itype]; lj3i = lj3[itype]; lj4i = lj4[itype]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; ni = 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]; respa_coul = 0; respa_lj = 0; if (rsq < cut_ljsq[itype][jtype]) { // lj frespa = 1.0; // check whether and how to compute respa corrections respa_flag = rsq < cut_in_on_sq ? 1 : 0; if (respa_flag && (rsq > cut_in_off_sq)) { double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff; frespa = 1-rsw*rsw*(3.0-2.0*rsw); } r2inv = 1.0/rsq; double rn = r2inv*r2inv*r2inv; if (respa_flag) respa_lj = ni == 0 ? // correct for respa frespa*rn*(rn*lj1i[jtype]-lj2i[jtype]) : frespa*rn*(rn*lj1i[jtype]-lj2i[jtype])*special_lj[ni]; if (order6) { // long-range form if (!ndisptablebits || rsq <= tabinnerdispsq) { double x2 = g2*rsq, a2 = 1.0/x2; x2 = a2*exp(-x2)*lj4i[jtype]; if (ni == 0) { forcelj = (rn*=rn)*lj1i[jtype]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq-respa_lj; if (eflag) evdwl = rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2; } else { // correct for special double f = special_lj[ni], t = rn*(1.0-f); forcelj = f*(rn *= rn)*lj1i[jtype]- g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*lj2i[jtype]-respa_lj; if (eflag) evdwl = f*rn*lj3i[jtype]-g6*((a2+1.0)*a2+0.5)*x2+t*lj4i[jtype]; } } else { // table real space union_int_float_t disp_t; disp_t.f = rsq; const int disp_k = (disp_t.i & ndispmask)>>ndispshiftbits; double f_disp = (rsq-rdisptable[disp_k])*drdisptable[disp_k]; if (ni == 0) { forcelj = (rn*=rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]-respa_lj; if (eflag) evdwl = rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]; } else { // special case double f = special_lj[ni], t = rn*(1.0-f); forcelj = f*(rn *= rn)*lj1i[jtype]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*lj4i[jtype]+t*lj2i[jtype]-respa_lj; if (eflag) evdwl = f*rn*lj3i[jtype]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*lj4i[jtype]+t*lj4i[jtype]; } } } else { // cut form if (ni == 0) { forcelj = rn*(rn*lj1i[jtype]-lj2i[jtype])-respa_lj; if (eflag) evdwl = rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype]; } else { // correct for special double f = special_lj[ni]; forcelj = f*rn*(rn*lj1i[jtype]-lj2i[jtype])-respa_lj; if (eflag) evdwl = f*(rn*(rn*lj3i[jtype]-lj4i[jtype])-offseti[jtype]); } } forcelj *= 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 (evflag) { fvirial = forcelj + respa_lj*r2inv; ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fvirial,delx,dely,delz); } } // adjust rsq and delxyz for off-site O charge(s) // ADDITIONAL REQEUST REQUIRED HERE!!!!! if (rsq < cut_coulsqplus) { if (itype == typeO || jtype == typeO) { if (jtype == typeO) { if (hneigh[j][0] < 0) { jH1 = atom->map(tag[j] + 1); jH2 = atom->map(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"); // set jH1,jH2 to closest image to O jH1 = domain->closest_image(j,jH1); jH2 = domain->closest_image(j,jH2); compute_newsite(x[j],x[jH1],x[jH2],newsite[j]); hneigh[j][0] = jH1; hneigh[j][1] = jH2; hneigh[j][2] = 1; } else { jH1 = hneigh[j][0]; jH2 = hneigh[j][1]; if (hneigh[j][2] == 0) { hneigh[j][2] = 1; compute_newsite(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; } // test current rsq against cutoff and compute Coulombic force if ((rsq < cut_coulsq) && order1) { frespa = 1.0; // check whether and how to compute respa corrections respa_flag = rsq < cut_in_on_sq ? 1 : 0; if (respa_flag && (rsq > cut_in_off_sq)) { double rsw = (sqrt(rsq)-cut_in_off)/cut_in_diff; frespa = 1-rsw*rsw*(3.0-2.0*rsw); } r2inv = 1.0 / rsq; if (!ncoultablebits || rsq <= tabinnersq) { // series real space double r = sqrt(rsq), s = qri*q[j]; if (respa_flag) // correct for respa respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni]; double x = g_ewald*r, t = 1.0/(1.0+EWALD_P*x); if (ni == 0) { s *= g_ewald*exp(-x*x); forcecoul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-respa_coul; if (eflag) ecoul = t; } else { // correct for special r = s*(1.0-special_coul[ni])/r; s *= g_ewald*exp(-x*x); forcecoul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-r-respa_coul; if (eflag) ecoul = t-r; } } // table real space else { if (respa_flag) { double r = sqrt(rsq), s = qri*q[j]; respa_coul = ni == 0 ? frespa*s/r : frespa*s/r*special_coul[ni]; } union_int_float_t t; t.f = rsq; const int k = (t.i & ncoulmask) >> ncoulshiftbits; double f = (t.f-rtable[k])*drtable[k], qiqj = qtmp*q[j]; if (ni == 0) { forcecoul = qiqj*(ftable[k]+f*dftable[k]); if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]); } else { // correct for special t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]); forcecoul = qiqj*(ftable[k]+f*dftable[k]-t.f); if (eflag) { t.f = (1.0-special_coul[ni])*(ptable[k]+f*dptable[k]); ecoul = qiqj*(etable[k]+f*detable[k]-t.f); } } } cforce = forcecoul * r2inv; fvirial = (forcecoul + respa_coul) * 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; key = 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 * fvirial; v[1] = x[i][1] * dely * fvirial; v[2] = x[i][2] * delz * fvirial; v[3] = x[i][0] * dely * fvirial; v[4] = x[i][0] * delz * fvirial; v[5] = x[i][1] * delz * fvirial; } vlist[n++] = i; } else { key += 1; fd[0] = delx*cforce; fd[1] = dely*cforce; fd[2] = delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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) { fd[0] = delx*fvirial; fd[1] = dely*fvirial; fd[2] = delz*fvirial; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[2]; xH1 = x[iH1]; xH2 = x[iH2]; 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 * fvirial; v[1] -= x[j][1] * dely * fvirial; v[2] -= x[j][2] * delz * fvirial; v[3] -= x[j][0] * dely * fvirial; v[4] -= x[j][0] * delz * fvirial; v[5] -= x[j][1] * delz * fvirial; } vlist[n++] = j; } else { key += 2; fd[0] = -delx*cforce; fd[1] = -dely*cforce; fd[2] = -delz*cforce; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[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) { fd[0] = -delx*fvirial; fd[1] = -dely*fvirial; fd[2] = -delz*fvirial; fO[0] = fd[0]*(1 - alpha); fO[1] = fd[1]*(1 - alpha); fO[2] = fd[2]*(1 - alpha); fH[0] = 0.5 * alpha * fd[0]; fH[1] = 0.5 * alpha * fd[1]; fH[2] = 0.5 * alpha * fd[2]; xH1 = x[jH1]; xH2 = x[jH2]; 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 (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha); } } } } } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairLJLongTIP4PLong::settings(int narg, char **arg) { if (narg < 8 || narg > 9) error->all(FLERR,"Illegal pair_style command"); ewald_off = 0; ewald_order = 0; options(arg, 6); options(++arg, 1); if (!comm->me && ewald_order&(1<<6)) error->warning(FLERR,"Mixing forced for lj coefficients"); if (!comm->me && ewald_order==((1<<1)|(1<<6))) error->warning(FLERR, "Using largest cutoff for pair_style lj/long/tip4p/long"); if (!((ewald_order^ewald_off)&(1<<1))) error->all(FLERR, "Coulomb cut not supported in pair_style lj/long/tip4p/long"); typeO = force->inumeric(FLERR,arg[1]); typeH = force->inumeric(FLERR,arg[2]); typeB = force->inumeric(FLERR,arg[3]); typeA = force->inumeric(FLERR,arg[4]); qdist = force->numeric(FLERR,arg[5]); cut_lj_global = force->numeric(FLERR,arg[6]); if (narg == 8) cut_coul = cut_lj_global; else cut_coul = force->numeric(FLERR,arg[7]); // reset cutoffs that have been explicitly set if (allocated) { int i,j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; } } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairLJLongTIP4PLong::init_style() { if (atom->tag_enable == 0) error->all(FLERR,"Pair style lj/long/tip4p/long requires atom IDs"); if (!force->newton_pair) error->all(FLERR,"Pair style lj/long/tip4p/long requires newton pair on"); if (!atom->q_flag) error->all(FLERR,"Pair style lj/long/tip4p/long requires atom attribute q"); 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"); PairLJLongCoulLong::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); } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairLJLongTIP4PLong::init_one(int i, int j) { double cut = PairLJLongCoulLong::init_one(i,j); // check that LJ epsilon = 0.0 for water H // set LJ cutoff to 0.0 for any interaction involving water H // so LJ term isn't calculated in compute() if ((i == typeH && epsilon[i][i] != 0.0)) error->all(FLERR,"Water H epsilon must be 0.0 for " "pair style lj/long/tip4p/long"); if (i == typeH || j == typeH) cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0; return cut; } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairLJLongTIP4PLong::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); fwrite(&ncoultablebits,sizeof(int),1,fp); fwrite(&tabinner,sizeof(double),1,fp); } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairLJLongTIP4PLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { utils::sfread(FLERR,&typeO,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&typeH,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&typeB,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&typeA,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&qdist,sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&cut_lj_global,sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&ncoultablebits,sizeof(int),1,fp,NULL,error); utils::sfread(FLERR,&tabinner,sizeof(double),1,fp,NULL,error); } 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); MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world); MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world); } /* ---------------------------------------------------------------------- compute position xM of fictitious charge site for O atom and 2 H atoms return it as xM ------------------------------------------------------------------------- */ void PairLJLongTIP4PLong::compute_newsite(double *xO, double *xH1, double *xH2, double *xM) { double delx1 = xH1[0] - xO[0]; double dely1 = xH1[1] - xO[1]; double delz1 = xH1[2] - xO[2]; double delx2 = xH2[0] - xO[0]; double dely2 = xH2[1] - xO[1]; double delz2 = xH2[2] - xO[2]; xM[0] = xO[0] + alpha * 0.5 * (delx1 + delx2); xM[1] = xO[1] + alpha * 0.5 * (dely1 + dely2); xM[2] = xO[2] + alpha * 0.5 * (delz1 + delz2); } /* ---------------------------------------------------------------------- */ void *PairLJLongTIP4PLong::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; const char *ids[] = { "B", "sigma", "epsilon", "ewald_order", "ewald_cut", "cut_coul", "ewald_mix", "cut_LJ", NULL}; void *ptrs[] = { lj4, sigma, epsilon, &ewald_order, &cut_coul, &cut_coul, &mix_flag, &cut_lj_global, NULL}; int i; i=0; while (ids[i] != NULL) { if (i <=2) dim = 2; else dim = 0; if (strcmp(ids[i],str) == 0) return ptrs[i]; ++i; } return NULL; } /* ---------------------------------------------------------------------- memory usage of hneigh ------------------------------------------------------------------------- */ double PairLJLongTIP4PLong::memory_usage() { double bytes = maxeatom * sizeof(double); bytes += maxvatom*6 * sizeof(double); bytes += 2 * nmax * sizeof(double); return bytes; }