#include "pair_lj_cut_coul_cut_tip4p.h" #include "universe.h" #include "force.h" #include "atom.h" #include "memory.h" #include "error.h" #include "math.h" #include "stdlib.h" #include "neighbor.h" #include "neigh_list.h" #include "domain.h" #include "angle.h" #include "bond.h" #include "math_const.h" #include "comm.h" using namespace LAMMPS_NS; using namespace MathConst; /* ---------------------------------------------------------------------- */ PairLJCutCoulCutTIP4P::PairLJCutCoulCutTIP4P(LAMMPS *lmp):Pair(lmp) { single_enable = 0; nmax = 0; hneigh = NULL; newsite = NULL; // 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; } /* ---------------------------------------------------------------------- */ PairLJCutCoulCutTIP4P::~PairLJCutCoulCutTIP4P() { if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cut_lj); memory->destroy(cut_ljsq); memory->destroy(epsilon); memory->destroy(sigma); memory->destroy(lj1); memory->destroy(lj2); memory->destroy(lj3); memory->destroy(lj4); memory->destroy(offset); } memory->destroy(hneigh); memory->destroy(newsite); } /* ---------------------------------------------------------------------- */ void PairLJCutCoulCutTIP4P::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul; double rsq,r2inv,r6inv,forcecoul,forcelj,factor_lj,factor_coul; int *ilist,*jlist,*numneigh,**firstneigh; int key; int n,vlist[6]; int iH1,iH2,jH1,jH2; double cforce; double fO[3],fH[3],fd[3],v[6],xH1[3],xH2[3]; double *x1,*x2; evdwl = ecoul = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; // 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; int *type = atom->type; double *special_lj = force->special_lj; double *special_coul = force->special_coul; int newton_pair = force->newton_pair; double qqrd2e = force->qqrd2e; 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) { hneigh[i][0] = iH1 = atom->map(atom->tag[i] + 1); hneigh[i][1] = iH2 = atom->map(atom->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(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(x[i],x[iH1],x[iH2],newsite[i]); } } x1 = newsite[i]; } 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 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(atom->tag[j] + 1); hneigh[j][1] = jH2 = atom->map(atom->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(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(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 = 1.0 / rsq; forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv); cforce = factor_coul * 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; 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++; fd[0] = delx*cforce; fd[1] = dely*cforce; fd[2] = delz*cforce; fO[0] = fd[0]*(1.0 - alpha); fO[1] = fd[1]*(1.0 - alpha); fO[2] = fd[2]*(1.0 - 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) { 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 { 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) { 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) { ecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv); ecoul *= factor_coul; } else ecoul = 0.0; if (evflag) ev_tally_tip4p(key,vlist,v,ecoul,alpha); } } } } } /* ---------------------------------------------------------------------- The settings method parses the pair_style command of the config file ---------------------------------------------------------------------- */ void PairLJCutCoulCutTIP4P::settings(int narg, char **arg) { // arg is an array of values in the config line like // "pair_style lj/cut/coul/cut/tip4p arg[0] arg[1] ... arg[n-1]" // The values arg[i] appear the same as in the line above; // to convert them into double or integer type, there are functions // 'double force->numeric(char *)' and 'int force->inumeric(char *)', // respectively. if( narg != 7 ) error->all(FLERR,"Illegal pairstyle 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]); // O-M distance in TIP4P-like models cut_lj_global = force->numeric(arg[5]); cut_coul = force->numeric(arg[6]); cut_coulsq = cut_coul * cut_coul; cut_coulsqplus = ( cut_coul + 2.0*qdist ) * ( cut_coul + 2.0*qdist ); 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 PairLJCutCoulCutTIP4P::init_style() { if (atom->tag_enable == 0) error->all(FLERR,"Pair style lj/cut/coul/cut/tip4p requires atom IDs"); if (!force->newton_pair) error->all(FLERR, "Pair style lj/cut/coul/cut/tip4p requires newton pair on"); if (!atom->q_flag) error->all(FLERR, "Pair style lj/cut/coul/cut/tip4p 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"); neighbor->request(this); // Calculating the alpha parameter double theta = force->angle->equilibrium_angle(typeA); double blen = force->bond->equilibrium_distance(typeB); alpha = qdist / (cos(0.5*theta) * blen); } /* ---------------------------------------------------------------------- The coeff method processes the pair_coeff commands(s) in config file ---------------------------------------------------------------------- */ void PairLJCutCoulCutTIP4P::coeff(int narg, char **arg) { if (narg < 4 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); // Only the cutoff values that are specified in pair_style command // will be used during the simulation. We will give a warning to user. if (narg == 5 || narg == 6) error->message(FLERR,"Only cutoffs set by pair_style are used in TIP4P"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; force->bounds(arg[0],atom->ntypes,ilo,ihi); force->bounds(arg[1],atom->ntypes,jlo,jhi); double epsilon_one = force->numeric(arg[2]); double sigma_one = force->numeric(arg[3]); int count = 0; for (int i = ilo; i <= ihi; i++) { for (int j = MAX(jlo,i); j <= jhi; j++) { epsilon[i][j] = epsilon_one; sigma[i][j] = sigma_one; cut_lj[i][j] = cut_lj_global; setflag[i][j] = 1; count++; } } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } void PairLJCutCoulCutTIP4P::allocate() { // Here i and j correspond to atomtypes defined by the read_data command; // the numbering in the arrays starts from 0, but the zero-th elements // aren't used, which is the reason why there is n+1 (not just n) in // the calls to the memory->create method. // // Both setflag and cutsq are declared in pair.h and are not allocated // in pair.cpp. allocated = 1; int n = atom->ntypes; memory->create(setflag,n+1,n+1,"pair:setflag"); for (int i = 1; i <= n; i++) for (int j = i; j <= n; j++) setflag[i][j] = 0; memory->create(cutsq,n+1,n+1,"pair:cutsq"); memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); memory->create(epsilon,n+1,n+1,"pair:epsilon"); memory->create(sigma,n+1,n+1,"pair:sigma"); memory->create(lj1,n+1,n+1,"pair:lj1"); memory->create(lj2,n+1,n+1,"pair:lj2"); memory->create(lj3,n+1,n+1,"pair:lj3"); memory->create(lj4,n+1,n+1,"pair:lj4"); memory->create(offset,n+1,n+1,"pair:offset"); } /* ---------------------------------------------------------------------- The function init_one returns the cutoff value for the interaction between a given pair of atomtypes; At least one element in cutsq array must be nonzero, otherwise the variable 'binsize' in Atom::setup_sort_bins is zero, which must not happen. This is why we override the Pair::init_style function here. The behavioor of Pair::init_style is to always return 0 (see pair.h). The cutsq array is filled in Pair::init, so we just need to provide an appropriate init_one function. ---------------------------------------------------------------------- */ double PairLJCutCoulCutTIP4P::init_one(int i, int j){ if (setflag[i][j] == 0) { epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], sigma[i][i],sigma[j][j]); sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); } // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist); cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); if (offset_flag) { double ratio = sigma[i][j] / cut_lj[i][j]; offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); } else offset[i][j] = 0.0; cut_ljsq[j][i] = cut_ljsq[i][j]; lj1[j][i] = lj1[i][j]; lj2[j][i] = lj2[i][j]; lj3[j][i] = lj3[i][j]; lj4[j][i] = lj4[i][j]; offset[j][i] = offset[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) || (j == typeH && epsilon[j][j] != 0.0)) error->all(FLERR,"Water H epsilon must be 0.0 for " "pair style lj/cut/coul/long/tip4p"); if (i == typeH || j == typeH) cut_ljsq[j][i] = cut_ljsq[i][j] = 0.0; return cut; } /* ---------------------------------------------------------------------- The method computes the x, y, and z coordinates of the virtual site of a TIP4P-like water molecule. ---------------------------------------------------------------------- */ void PairLJCutCoulCutTIP4P::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]; 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); 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 PairLJCutCoulCutTIP4P::write_restart(FILE *fp) { write_restart_settings(fp); int i,j; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]){ fwrite(&epsilon[i][j],sizeof(double),1,fp); fwrite(&sigma[i][j],sizeof(double),1,fp); fwrite(&cut_lj[i][j],sizeof(double),1,fp); } } } } void PairLJCutCoulCutTIP4P::read_restart(FILE *fp) { read_restart_settings(fp); allocate(); int i,j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { fread(&epsilon[i][j],sizeof(double),1,fp); fread(&sigma[i][j],sizeof(double),1,fp); fread(&cut_lj[i][j],sizeof(double),1,fp); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); } } } } void PairLJCutCoulCutTIP4P::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(&cut_coulsq,sizeof(double),1,fp); fwrite(&cut_coulsqplus,sizeof(double),1,fp); } void PairLJCutCoulCutTIP4P::read_restart_settings(FILE *fp) { int me = comm->me; if (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(&cut_coulsq,sizeof(double),1,fp); fread(&cut_coulsqplus,sizeof(double),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(&cut_coulsq,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_coulsqplus,1,MPI_DOUBLE,0,world); }