diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index dc34f39655..60b988926a 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -1,711 +1,711 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_lj_class2.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.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; -} - -/* ---------------------------------------------------------------------- */ - -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 = 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 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; - 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 cut_one = cut_global; - if (narg == 5) cut_one = force->numeric(FLERR,arg[4]); - - 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 = NULL; -} - -/* ---------------------------------------------------------------------- - 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) 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[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[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) { - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - } - 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 NULL; -} \ No newline at end of file +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_class2.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.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; +} + +/* ---------------------------------------------------------------------- */ + +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 = 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 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; + 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 cut_one = cut_global; + if (narg == 5) cut_one = force->numeric(FLERR,arg[4]); + + 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 = NULL; +} + +/* ---------------------------------------------------------------------- + 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) 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[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[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) { + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + 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 NULL; +} diff --git a/src/CLASS2/pair_lj_class2.h b/src/CLASS2/pair_lj_class2.h index 5bb2a1f0d9..7680498a07 100644 --- a/src/CLASS2/pair_lj_class2.h +++ b/src/CLASS2/pair_lj_class2.h @@ -70,4 +70,3 @@ E: Pair cutoff < Respa interior cutoff One or more pairwise cutoffs are too short to use with the specified rRESPA cutoffs. */ -