/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://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. ------------------------------------------------------------------------- */ #include "pair_lj_class2.h" #include #include #include "atom.h" #include "comm.h" #include "force.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" #include "update.h" #include "respa.h" #include "math_const.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace MathConst; /* ---------------------------------------------------------------------- */ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) { respa_enable = 1; writedata = 1; centroidstressflag = 1; } /* ---------------------------------------------------------------------- */ PairLJClass2::~PairLJClass2() { if (copymode) return; if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cut); memory->destroy(epsilon); memory->destroy(sigma); memory->destroy(lj1); memory->destroy(lj2); memory->destroy(lj3); memory->destroy(lj4); memory->destroy(offset); } } /* ---------------------------------------------------------------------- */ void PairLJClass2::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,rinv,r2inv,r3inv,r6inv,forcelj,factor_lj; int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; int newton_pair = force->newton_pair; 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]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[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; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (newton_pair || j < nlocal) { f[j][0] -= delx*fpair; f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } if (eflag) { evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) - offset[itype][jtype]; evdwl *= factor_lj; } if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- */ void PairLJClass2::compute_inner() { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpair; double rsq,rinv,r2inv,r3inv,r6inv,forcelj,factor_lj,rsw; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; int newton_pair = force->newton_pair; inum = list->inum_inner; ilist = list->ilist_inner; numneigh = list->numneigh_inner; firstneigh = list->firstneigh_inner; 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; // loop over neighbors of my atoms for (ii = 0; ii < inum; ii++) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[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; if (rsq < cut_out_off_sq) { r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; jtype = type[j]; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; if (rsq > cut_out_on_sq) { rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw); } f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (newton_pair || j < nlocal) { f[j][0] -= delx*fpair; f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } } } } } /* ---------------------------------------------------------------------- */ void PairLJClass2::compute_middle() { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpair; double rsq,rinv,r2inv,r3inv,r6inv,forcelj,factor_lj,rsw; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; int newton_pair = force->newton_pair; inum = list->inum_middle; ilist = list->ilist_middle; numneigh = list->numneigh_middle; firstneigh = list->firstneigh_middle; 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; // loop over neighbors of my atoms for (ii = 0; ii < inum; ii++) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[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; if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) { r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; jtype = type[j]; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; if (rsq < cut_in_on_sq) { rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; fpair *= rsw*rsw*(3.0 - 2.0*rsw); } if (rsq > cut_out_on_sq) { rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff; fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0); } f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (newton_pair || j < nlocal) { f[j][0] -= delx*fpair; f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } } } } } /* ---------------------------------------------------------------------- */ void PairLJClass2::compute_outer(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,rinv,r2inv,r3inv,r6inv,forcelj,factor_lj,rsw; int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_lj = force->special_lj; int newton_pair = force->newton_pair; inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; 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; // loop over neighbors of my atoms for (ii = 0; ii < inum; ii++) { i = ilist[ii]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; itype = type[i]; jlist = firstneigh[i]; jnum = numneigh[i]; for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[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]) { if (rsq > cut_in_off_sq) { r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; if (rsq < cut_in_on_sq) { rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; fpair *= rsw*rsw*(3.0 - 2.0*rsw); } f[i][0] += delx*fpair; f[i][1] += dely*fpair; f[i][2] += delz*fpair; if (newton_pair || j < nlocal) { f[j][0] -= delx*fpair; f[j][1] -= dely*fpair; f[j][2] -= delz*fpair; } } if (eflag) { r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) - offset[itype][jtype]; evdwl *= factor_lj; } if (vflag) { if (rsq <= cut_in_off_sq) { r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fpair = factor_lj*forcelj*r2inv; } else if (rsq < cut_in_on_sq) fpair = factor_lj*forcelj*r2inv; } if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } } /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ void PairLJClass2::allocate() { 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,n+1,n+1,"pair:cut"); 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"); } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairLJClass2::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); cut_global = utils::numeric(FLERR,arg[0],false,lmp); // 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[i][j] = cut_global; } } /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ void PairLJClass2::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); double cut_one = cut_global; if (narg == 5) cut_one = utils::numeric(FLERR,arg[4],false,lmp); 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[i][j] = cut_one; setflag[i][j] = 1; count++; } } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairLJClass2::init_style() { // request regular or rRESPA neighbor list int irequest; int respa = 0; if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; } irequest = neighbor->request(this,instance_me); if (respa >= 1) { neighbor->requests[irequest]->respaouter = 1; neighbor->requests[irequest]->respainner = 1; } if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; // set rRESPA cutoffs if (strstr(update->integrate_style,"respa") && ((Respa *) update->integrate)->level_inner >= 0) cut_respa = ((Respa *) update->integrate)->cutoff; else cut_respa = nullptr; } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairLJClass2::init_one(int i, int j) { // always mix epsilon,sigma via sixthpower rules // mix distance via user-defined rule if (setflag[i][j] == 0) { epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) * pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) / (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0)); sigma[i][j] = pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0); cut[i][j] = mix_distance(cut[i][i],cut[j][j]); } lj1[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j],9.0); lj2[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j],6.0); lj3[i][j] = 2.0 * epsilon[i][j] * pow(sigma[i][j],9.0); lj4[i][j] = 3.0 * epsilon[i][j] * pow(sigma[i][j],6.0); if (offset_flag && (cut[i][j] > 0.0)) { double ratio = sigma[i][j] / cut[i][j]; offset[i][j] = epsilon[i][j] * (2.0*pow(ratio,9.0) - 3.0*pow(ratio,6.0)); } else offset[i][j] = 0.0; 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 interior rRESPA cutoff if (cut_respa && cut[i][j] < cut_respa[3]) error->all(FLERR,"Pair cutoff < Respa interior cutoff"); // compute I,J contribution to long-range tail correction // count total # of atoms of type I and J via Allreduce if (tail_flag) { int *type = atom->type; int nlocal = atom->nlocal; double count[2],all[2]; count[0] = count[1] = 0.0; for (int k = 0; k < nlocal; k++) { if (type[k] == i) count[0] += 1.0; if (type[k] == j) count[1] += 1.0; } MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j]; double sig6 = sig3*sig3; double rc3 = cut[i][j]*cut[i][j]*cut[i][j]; double rc6 = rc3*rc3; etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 * (sig3 - 3.0*rc3) / (3.0*rc6); ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 * (sig3 - 2.0*rc3) / rc6; } return cut[i][j]; } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairLJClass2::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[i][j],sizeof(double),1,fp); } } } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairLJClass2::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairLJClass2::write_restart_settings(FILE *fp) { fwrite(&cut_global,sizeof(double),1,fp); fwrite(&offset_flag,sizeof(int),1,fp); fwrite(&mix_flag,sizeof(int),1,fp); fwrite(&tail_flag,sizeof(int),1,fp); } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairLJClass2::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error); } MPI_Bcast(&cut_global,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(&tail_flag,1,MPI_INT,0,world); } /* ---------------------------------------------------------------------- proc 0 writes to data file ------------------------------------------------------------------------- */ void PairLJClass2::write_data(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]); } /* ---------------------------------------------------------------------- proc 0 writes all pairs to data file ------------------------------------------------------------------------- */ void PairLJClass2::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut[i][j]); } /* ---------------------------------------------------------------------- */ double PairLJClass2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*factor_coul*/, double factor_lj, double &fforce) { double r2inv,rinv,r3inv,r6inv,forcelj,philj; r2inv = 1.0/rsq; rinv = sqrt(r2inv); r3inv = r2inv*rinv; r6inv = r3inv*r3inv; forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]); fforce = factor_lj*forcelj*r2inv; philj = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) - offset[itype][jtype]; return factor_lj*philj; } /* ---------------------------------------------------------------------- */ void *PairLJClass2::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"epsilon") == 0) return (void *) epsilon; if (strcmp(str,"sigma") == 0) return (void *) sigma; return nullptr; }