/* ---------------------------------------------------------------------- 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 author: Cassiano Aimoli (aimoli@gmail.com) ------------------------------------------------------------------------- */ #include "pair_mie_cut.h" #include #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" #include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; /* ---------------------------------------------------------------------- */ PairMIECut::PairMIECut(LAMMPS *lmp) : Pair(lmp) { respa_enable = 1; cut_respa = NULL; } /* ---------------------------------------------------------------------- */ PairMIECut::~PairMIECut() { if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cut); memory->destroy(epsilon); memory->destroy(sigma); memory->destroy(gamR); memory->destroy(gamA); memory->destroy(Cmie); memory->destroy(mie1); memory->destroy(mie2); memory->destroy(mie3); memory->destroy(mie4); memory->destroy(offset); } } /* ---------------------------------------------------------------------- */ void PairMIECut::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,r2inv,rgamR,rgamA,forcemie,factor_mie; 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_mie = 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_mie = special_mie[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; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fpair = factor_mie*forcemie*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 = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) - offset[itype][jtype]; evdwl *= factor_mie; } if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- */ void PairMIECut::compute_inner() { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpair; double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie,rsw; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_mie = 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_mie = special_mie[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) { jtype = type[j]; r2inv = 1.0/rsq; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fpair = factor_mie*forcemie*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 PairMIECut::compute_middle() { int i,j,ii,jj,inum,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpair; double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie,rsw; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; double **f = atom->f; int *type = atom->type; int nlocal = atom->nlocal; double *special_mie = 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_mie = special_mie[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) { jtype = type[j]; r2inv = 1.0/rsq; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fpair = factor_mie*forcemie*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 PairMIECut::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,r2inv,rgamR,rgamA,forcemie,factor_mie,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_mie = 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_mie = special_mie[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; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fpair = factor_mie*forcemie*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; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); evdwl = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) - offset[itype][jtype]; evdwl *= factor_mie; } if (vflag) { if (rsq <= cut_in_off_sq) { r2inv = 1.0/rsq; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fpair = factor_mie*forcemie*r2inv; } else if (rsq < cut_in_on_sq) fpair = factor_mie*forcemie*r2inv; } if (evflag) ev_tally(i,j,nlocal,newton_pair, evdwl,0.0,fpair,delx,dely,delz); } } } } /* ---------------------------------------------------------------------- allocate all arrays ------------------------------------------------------------------------- */ void PairMIECut::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(gamR,n+1,n+1,"pair:gamR"); memory->create(gamA,n+1,n+1,"pair:gamA"); memory->create(Cmie,n+1,n+1,"pair:Cmie"); memory->create(mie1,n+1,n+1,"pair:mie1"); memory->create(mie2,n+1,n+1,"pair:mie2"); memory->create(mie3,n+1,n+1,"pair:mie3"); memory->create(mie4,n+1,n+1,"pair:mie4"); memory->create(offset,n+1,n+1,"pair:offset"); } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairMIECut::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); cut_global = force->numeric(FLERR,arg[0]); // 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 PairMIECut::coeff(int narg, char **arg) { if (narg < 6 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); double epsilon_one = force->numeric(FLERR,arg[2]); double sigma_one = force->numeric(FLERR,arg[3]); double gamR_one = force->numeric(FLERR,arg[4]); double gamA_one = force->numeric(FLERR,arg[5]); double cut_one = cut_global; if (narg == 7) cut_one = force->numeric(FLERR,arg[6]); 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; gamR[i][j] = gamR_one; gamA[i][j] = gamA_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 PairMIECut::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 = NULL; } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairMIECut::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]); gamR[i][j] = mix_distance(gamR[i][i],gamR[j][j]); gamA[i][j] = mix_distance(gamA[i][i],gamA[j][j]); cut[i][j] = mix_distance(cut[i][i],cut[j][j]); } gamA[j][i] = gamA[i][j]; gamR[j][i] = gamR[i][j]; Cmie[i][j] = (gamR[i][j]/(gamR[i][j]-gamA[i][j]) * pow((gamR[i][j]/gamA[i][j]), (gamA[i][j]/(gamR[i][j]-gamA[i][j])))); mie1[i][j] = Cmie[i][j] * gamR[i][j]* epsilon[i][j] * pow(sigma[i][j],gamR[i][j]); mie2[i][j] = Cmie[i][j] * gamA[i][j] * epsilon[i][j] * pow(sigma[i][j],gamA[i][j]); mie3[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamR[i][j]); mie4[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamA[i][j]); if (offset_flag && (cut[i][j] > 0.0)) { double ratio = sigma[i][j] / cut[i][j]; offset[i][j] = Cmie[i][j] * epsilon[i][j] * (pow(ratio,gamR[i][j]) - pow(ratio,gamA[i][j])); } else offset[i][j] = 0.0; mie1[j][i] = mie1[i][j]; mie2[j][i] = mie2[i][j]; mie3[j][i] = mie3[i][j]; mie4[j][i] = mie4[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 siggamA = pow(sigma[i][j],gamA[i][j]); double siggamR = pow(sigma[i][j],gamR[i][j]); double rcgamA = pow(cut[i][j],(gamA[i][j]-3.0)); double rcgamR = pow(cut[i][j],(gamR[i][j]-3.0)); etail_ij = Cmie[i][j]*2.0*MY_PI*all[0]*all[1]*epsilon[i][j]* (siggamR/((gamR[i][j]-3.0)*rcgamR)-siggamA/((gamA[i][j]-3.0)*rcgamA)); ptail_ij = Cmie[i][j]*2.0*MY_PI*all[0]*all[1]*epsilon[i][j]/3.0* ((gamR[i][j]/(gamR[i][j]-3.0))*siggamR/rcgamR- (gamA[i][j]/(gamA[i][j]-3.0))*siggamA/rcgamA); } return cut[i][j]; } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairMIECut::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(&gamR[i][j],sizeof(double),1,fp); fwrite(&gamA[i][j],sizeof(double),1,fp); fwrite(&cut[i][j],sizeof(double),1,fp); } } } /* ---------------------------------------------------------------------- proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ void PairMIECut::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,NULL,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,NULL,error); utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&gamR[i][j],sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&gamA[i][j],sizeof(double),1,fp,NULL,error); utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error); } MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&gamR[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&gamA[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } } } /* ---------------------------------------------------------------------- proc 0 writes to restart file ------------------------------------------------------------------------- */ void PairMIECut::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 PairMIECut::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { utils::sfread(FLERR,&cut_global,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,&tail_flag,sizeof(int),1,fp,NULL,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); } /* ---------------------------------------------------------------------- */ double PairMIECut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*factor_coul*/, double factor_mie, double &fforce) { double r2inv,rgamR,rgamA,forcemie,phimie; r2inv = 1.0/rsq; rgamA = pow(r2inv,(gamA[itype][jtype]/2.0)); rgamR = pow(r2inv,(gamR[itype][jtype]/2.0)); forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA); fforce = factor_mie*forcemie*r2inv; phimie = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) - offset[itype][jtype]; return factor_mie*phimie; } /* ---------------------------------------------------------------------- */ void *PairMIECut::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"epsilon") == 0) return (void *) epsilon; if (strcmp(str,"sigma") == 0) return (void *) sigma; if (strcmp(str,"gamR") == 0) return (void *) gamR; if (strcmp(str,"gamA") == 0) return (void *) gamA; return NULL; }