diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 054580ed04..e4c3f63b95 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -1,514 +1,514 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "pair_lj_cut_coul_cut_soft.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; -using namespace MathConst; - -/* ---------------------------------------------------------------------- */ - -PairLJCutCoulCutSoft::PairLJCutCoulCutSoft(LAMMPS *lmp) : Pair(lmp) -{ - writedata = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairLJCutCoulCutSoft::~PairLJCutCoulCutSoft() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(cut_coul); - memory->destroy(cut_coulsq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lambda); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double rsq,forcecoul,forcelj,factor_coul,factor_lj; - double denc, denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - 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]; - 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]; - - if (rsq < cutsq[itype][jtype]) { - - if (rsq < cut_coulsq[itype][jtype]) { - denc = sqrt(lj4[itype][jtype] + rsq); - forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); - } else forcecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - - fpair = factor_coul*forcecoul + factor_lj*forcelj; - - 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) { - if (rsq < cut_coulsq[itype][jtype]) - ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; - else ecoul = 0.0; - if (rsq < cut_ljsq[itype][jtype]) { - evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - evdwl *= factor_lj; - } else evdwl = 0.0; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,ecoul,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::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_lj,n+1,n+1,"pair:cut_lj"); - memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); - memory->create(cut_coul,n+1,n+1,"pair:cut_coul"); - memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lambda,n+1,n+1,"pair:lambda"); - 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 PairLJCutCoulCutSoft::settings(int narg, char **arg) -{ - if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); - - nlambda = force->numeric(FLERR,arg[0]); - alphalj = force->numeric(FLERR,arg[1]); - alphac = force->numeric(FLERR,arg[2]); - - cut_lj_global = force->numeric(FLERR,arg[3]); - if (narg == 4) cut_coul_global = cut_lj_global; - else cut_coul_global = force->numeric(FLERR,arg[4]); - - // reset cutoffs that have been explicitly set - - 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; - cut_coul[i][j] = cut_coul_global; - } - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::coeff(int narg, char **arg) -{ - if (narg < 5 || narg > 7) - error->all(FLERR,"Incorrect args for pair coefficients"); - 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(FLERR,arg[2]); - double sigma_one = force->numeric(FLERR,arg[3]); - double lambda_one = force->numeric(FLERR,arg[4]); - - double cut_lj_one = cut_lj_global; - double cut_coul_one = cut_coul_global; - if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]); - if (narg == 7) cut_coul_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; - lambda[i][j] = lambda_one; - cut_lj[i][j] = cut_lj_one; - cut_coul[i][j] = cut_coul_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::init_style() -{ - if (!atom->q_flag) - error->all(FLERR,"Pair style lj/cut/coul/cut/soft requires atom attribute q"); - - neighbor->request(this,instance_me); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairLJCutCoulCutSoft::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]); - if (lambda[i][i] != lambda[j][j]) - error->all(FLERR,"Pair lj/cut/coul/cut/soft different lambda values in mix"); - lambda[i][j] = lambda[i][i]; - cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); - cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]); - } - - double cut = MAX(cut_lj[i][j],cut_coul[i][j]); - cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; - cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j]; - - lj1[i][j] = pow(lambda[i][j], nlambda); - lj2[i][j] = pow(sigma[i][j], 6.0); - lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); - lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); - - if (offset_flag) { - double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); - offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); - } else offset[i][j] = 0.0; - - epsilon[j][i] = epsilon[i][j]; - sigma[j][i] = sigma[i][j]; - lambda[j][i] = lambda[i][j]; - cut_ljsq[j][i] = cut_ljsq[i][j]; - cut_coulsq[j][i] = cut_coulsq[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]; - - // 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 sig2 = sigma[i][j]*sigma[i][j]; - double sig6 = sig2*sig2*sig2; - double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; - double rc6 = rc3*rc3; - double rc9 = rc3*rc6; - etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); - ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); - } - - return cut; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::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(&lambda[i][j],sizeof(double),1,fp); - fwrite(&cut_lj[i][j],sizeof(double),1,fp); - fwrite(&cut_coul[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::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(&lambda[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - fread(&cut_coul[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(&lambda[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::write_restart_settings(FILE *fp) -{ - fwrite(&nlambda,sizeof(double),1,fp); - fwrite(&alphalj,sizeof(double),1,fp); - fwrite(&alphac,sizeof(double),1,fp); - - fwrite(&cut_lj_global,sizeof(double),1,fp); - fwrite(&cut_coul_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 PairLJCutCoulCutSoft::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul_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(&nlambda,1,MPI_DOUBLE,0,world); - MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); - MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); - - MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul_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 PairLJCutCoulCutSoft::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairLJCutCoulCutSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], - lambda[i][j],cut_lj[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairLJCutCoulCutSoft::single(int i, int j, int itype, int jtype, - double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double forcecoul,forcelj,phicoul,philj; - double denc, denlj, r4sig6; - - if (rsq < cut_coulsq[itype][jtype]) { - denc = sqrt(lj4[itype][jtype] + rsq); - forcecoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / - (denc*denc*denc); - } else forcecoul = 0.0; - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - fforce = factor_coul*forcecoul + factor_lj*forcelj; - - double eng = 0.0; - if (rsq < cut_coulsq[itype][jtype]) { - phicoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; - eng += factor_coul*phicoul; - } - if (rsq < cut_ljsq[itype][jtype]) { - philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - eng += factor_lj*philj; - } - - return eng; -} - -/* ---------------------------------------------------------------------- */ - -void *PairLJCutCoulCutSoft::extract(const char *str, int &dim) -{ - dim = 0; - if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; - dim = 2; - if (strcmp(str,"epsilon") == 0) return (void *) epsilon; - if (strcmp(str,"sigma") == 0) return (void *) sigma; - if (strcmp(str,"lambda") == 0) return (void *) lambda; - return NULL; -} +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_cut_coul_cut_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulCutSoft::PairLJCutCoulCutSoft(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulCutSoft::~PairLJCutCoulCutSoft() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(cut_coul); + memory->destroy(cut_coulsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,forcecoul,forcelj,factor_coul,factor_lj; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + 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]; + 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]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq[itype][jtype]) { + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + + fpair = factor_coul*forcecoul + factor_lj*forcelj; + + 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) { + if (rsq < cut_coulsq[itype][jtype]) + ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::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_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(cut_coul,n+1,n+1,"pair:cut_coul"); + memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lambda,n+1,n+1,"pair:lambda"); + 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 PairLJCutCoulCutSoft::settings(int narg, char **arg) +{ + if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + alphac = force->numeric(FLERR,arg[2]); + + cut_lj_global = force->numeric(FLERR,arg[3]); + if (narg == 4) cut_coul_global = cut_lj_global; + else cut_coul_global = force->numeric(FLERR,arg[4]); + + // reset cutoffs that have been explicitly set + + 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; + cut_coul[i][j] = cut_coul_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 7) + error->all(FLERR,"Incorrect args for pair coefficients"); + 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(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + + double cut_lj_one = cut_lj_global; + double cut_coul_one = cut_coul_global; + if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]); + if (narg == 7) cut_coul_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; + lambda[i][j] = lambda_one; + cut_lj[i][j] = cut_lj_one; + cut_coul[i][j] = cut_coul_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style lj/cut/coul/cut/soft requires atom attribute q"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCutCoulCutSoft::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]); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/cut/coul/cut/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul[i][j]); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j]; + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag) { + double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); + offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + cut_ljsq[j][i] = cut_ljsq[i][j]; + cut_coulsq[j][i] = cut_coulsq[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]; + + // 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 sig2 = sigma[i][j]*sigma[i][j]; + double sig6 = sig2*sig2*sig2; + double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + double rc6 = rc3*rc3; + double rc9 = rc3*rc6; + etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); + ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::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(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + fwrite(&cut_coul[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::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(&lambda[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + fread(&cut_coul[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(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&alphac,sizeof(double),1,fp); + + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul_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 PairLJCutCoulCutSoft::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&alphac,sizeof(double),1,fp); + + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul_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(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); + + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul_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 PairLJCutCoulCutSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJCutCoulCutSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCutCoulCutSoft::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double forcecoul,forcelj,phicoul,philj; + double denc, denlj, r4sig6; + + if (rsq < cut_coulsq[itype][jtype]) { + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / + (denc*denc*denc); + } else forcecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + fforce = factor_coul*forcecoul + factor_lj*forcelj; + + double eng = 0.0; + if (rsq < cut_coulsq[itype][jtype]) { + phicoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; + eng += factor_coul*phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + eng += factor_lj*philj; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJCutCoulCutSoft::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + return NULL; +} diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 570e55b501..a9f3e1d683 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -1,955 +1,955 @@ -/* ---------------------------------------------------------------------- - 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: Paul Crozier (SNL) - Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "pair_lj_cut_coul_long_soft.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; -using namespace MathConst; - -#define EWALD_F 1.12837917 -#define EWALD_P 0.3275911 -#define A1 0.254829592 -#define A2 -0.284496736 -#define A3 1.421413741 -#define A4 -1.453152027 -#define A5 1.061405429 - -/* ---------------------------------------------------------------------- */ - -PairLJCutCoulLongSoft::PairLJCutCoulLongSoft(LAMMPS *lmp) : Pair(lmp) -{ - ewaldflag = pppmflag = 1; - respa_enable = 1; - writedata = 1; - qdist = 0.0; -} - -/* ---------------------------------------------------------------------- */ - -PairLJCutCoulLongSoft::~PairLJCutCoulLongSoft() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lambda); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::compute(int eflag, int vflag) -{ - int i,ii,j,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; - double grij,expm2,prefactor,t,erfc; - double denc, denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - 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]; - 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]; - - if (rsq < cutsq[itype][jtype]) { - - if (rsq < cut_coulsq) { - r = sqrt(rsq); - grij = g_ewald * r; - expm2 = exp(-grij*grij); - t = 1.0 / (1.0 + EWALD_P*grij); - erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; - - denc = sqrt(lj4[itype][jtype] + rsq); - prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); - - forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; - } else forcecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - - fpair = forcecoul + factor_lj*forcelj; - - 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) { - if (rsq < cut_coulsq) { - prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; - ecoul = prefactor*erfc; - if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; - } else ecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype]) { - evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - evdwl *= factor_lj; - } else evdwl = 0.0; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,ecoul,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::compute_inner() -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; - double rsq,forcecoul,forcelj,factor_coul,factor_lj; - double rsw; - double denc, denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - double qqrd2e = force->qqrd2e; - - inum = listinner->inum; - ilist = listinner->ilist; - numneigh = listinner->numneigh; - firstneigh = listinner->firstneigh; - - 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]; - qtmp = q[i]; - 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)]; - 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; - - if (rsq < cut_out_off_sq) { - jtype = type[j]; - - denc = sqrt(lj4[itype][jtype] + rsq); - forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; - - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - - fpair = forcecoul + factor_lj*forcelj; - - 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 PairLJCutCoulLongSoft::compute_middle() -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; - double rsq,forcecoul,forcelj,factor_coul,factor_lj; - double rsw; - double denc, denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - double qqrd2e = force->qqrd2e; - - inum = listmiddle->inum; - ilist = listmiddle->ilist; - numneigh = listmiddle->numneigh; - firstneigh = listmiddle->firstneigh; - - 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]; - qtmp = q[i]; - 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)]; - 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; - - if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) { - jtype = type[j]; - - denc = sqrt(lj4[itype][jtype] + rsq); - forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; - - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - - fpair = forcecoul + factor_lj*forcelj; - - 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 PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; - double grij,expm2,fprefactor,eprefactor,t,erfc; - double rsw; - double denc, denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_coul = force->special_coul; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - double qqrd2e = force->qqrd2e; - - inum = listouter->inum; - ilist = listouter->ilist; - numneigh = listouter->numneigh; - firstneigh = listouter->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]; - qtmp = q[i]; - 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)]; - factor_coul = special_coul[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - - if (rsq < cut_coulsq) { - r = sqrt(rsq); - grij = g_ewald * r; - expm2 = exp(-grij*grij); - t = 1.0 / (1.0 + EWALD_P*grij); - erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; - - denc = sqrt(lj4[itype][jtype] + rsq); - fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); - - forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2 - 1.0); - - if (rsq > cut_in_off_sq) { - if (rsq < cut_in_on_sq) { - rsw = (r - cut_in_off)/cut_in_diff; - forcecoul += fprefactor*rsw*rsw*(3.0 - 2.0*rsw); - if (factor_coul < 1.0) - forcecoul -= - (1.0-factor_coul)*fprefactor*rsw*rsw*(3.0 - 2.0*rsw); - } else { - forcecoul += fprefactor; - if (factor_coul < 1.0) - forcecoul -= (1.0-factor_coul)*fprefactor; - } - } - } else forcecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - if (rsq < cut_in_on_sq) { - rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; - forcelj *= rsw*rsw*(3.0 - 2.0*rsw); - } - } else forcelj = 0.0; - - fpair = forcecoul + forcelj; - - 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) { - if (rsq < cut_coulsq) { - eprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; - ecoul = eprefactor*erfc; - if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*eprefactor; - } else ecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype]) { - evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - evdwl *= factor_lj; - } else evdwl = 0.0; - } - - if (vflag) { - if (rsq < cut_coulsq) { - forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*fprefactor; - } else forcecoul = 0.0; - - if (rsq <= cut_in_off_sq) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else if (rsq < cut_in_on_sq) { - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } - fpair = forcecoul + factor_lj*forcelj; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,ecoul,fpair,delx,dely,delz); - } - } - } -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::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_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(lambda,n+1,n+1,"pair:lambda"); - 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 PairLJCutCoulLongSoft::settings(int narg, char **arg) -{ - if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); - - nlambda = force->numeric(FLERR,arg[0]); - alphalj = force->numeric(FLERR,arg[1]); - alphac = force->numeric(FLERR,arg[2]); - - cut_lj_global = force->numeric(FLERR,arg[3]); - if (narg == 4) cut_coul = cut_lj_global; - else cut_coul = force->numeric(FLERR,arg[4]); - - // reset cutoffs that have been explicitly set - - 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; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::coeff(int narg, char **arg) -{ - if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); - 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(FLERR,arg[2]); - double sigma_one = force->numeric(FLERR,arg[3]); - double lambda_one = force->numeric(FLERR,arg[4]); - - double cut_lj_one = cut_lj_global; - if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]); - - 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; - lambda[i][j] = lambda_one; - cut_lj[i][j] = cut_lj_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::init_style() -{ - if (!atom->q_flag) - error->all(FLERR,"Pair style lj/cut/coul/long/soft requires atom attribute q"); - - // request regular or rRESPA neighbor lists - - int irequest; - - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { - int respa = 0; - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; - - if (respa == 0) irequest = neighbor->request(this,instance_me); - else if (respa == 1) { - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respainner = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 3; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respaouter = 1; - } else { - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respainner = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 2; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respamiddle = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 3; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respaouter = 1; - } - - } else irequest = neighbor->request(this,instance_me); - - cut_coulsq = cut_coul * cut_coul; - - // 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; - - // insure use of KSpace long-range solver, set g_ewald - - if (force->kspace == NULL) - error->all(FLERR,"Pair style requires a KSpace style"); - g_ewald = force->kspace->g_ewald; -} - -/* ---------------------------------------------------------------------- - neighbor callback to inform pair style of neighbor list to use - regular or rRESPA -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::init_list(int id, NeighList *ptr) -{ - if (id == 0) list = ptr; - else if (id == 1) listinner = ptr; - else if (id == 2) listmiddle = ptr; - else if (id == 3) listouter = ptr; -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairLJCutCoulLongSoft::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]); - if (lambda[i][i] != lambda[j][j]) - error->all(FLERR,"Pair lj/cut/coul/long/soft different lambda values in mix"); - lambda[i][j] = lambda[i][i]; - 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] = pow(lambda[i][j], nlambda); - lj2[i][j] = pow(sigma[i][j], 6.0); - lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); - lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); - - if (offset_flag) { - double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); - offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); - } else offset[i][j] = 0.0; - - epsilon[j][i] = epsilon[i][j]; - sigma[j][i] = sigma[i][j]; - lambda[j][i] = lambda[i][j]; - 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 interior rRESPA cutoff - - if (cut_respa && MIN(cut_lj[i][j],cut_coul) < 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 sig2 = sigma[i][j]*sigma[i][j]; - double sig6 = sig2*sig2*sig2; - double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; - double rc6 = rc3*rc3; - double rc9 = rc3*rc6; - etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); - ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); - } - - return cut; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp); - fwrite(&cut_lj[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::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(&lambda[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(&lambda[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::write_restart_settings(FILE *fp) -{ - fwrite(&nlambda,sizeof(double),1,fp); - fwrite(&alphalj,sizeof(double),1,fp); - fwrite(&alphac,sizeof(double),1,fp); - - fwrite(&cut_lj_global,sizeof(double),1,fp); - fwrite(&cut_coul,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); - fwrite(&tail_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - fread(&alphac,sizeof(double),1,fp); - - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,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(&nlambda,1,MPI_DOUBLE,0,world); - MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); - MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); - - MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); - MPI_Bcast(&offset_flag,1,MPI_INT,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); - MPI_Bcast(&tail_flag,1,MPI_INT,0,world); -} - - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairLJCutCoulLongSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], - lambda[i][j],cut_lj[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairLJCutCoulLongSoft::single(int i, int j, int itype, int jtype, - double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double r,grij,expm2,t,erfc,prefactor; - double forcecoul,forcelj,phicoul,philj; - double denc, denlj, r4sig6; - - if (rsq < cut_coulsq) { - r = sqrt(rsq); - grij = g_ewald * r; - expm2 = exp(-grij*grij); - t = 1.0 / (1.0 + EWALD_P*grij); - erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; - - denc = sqrt(lj4[itype][jtype] + rsq); - prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / - (denc*denc*denc); - - forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; - } else forcecoul = 0.0; - - if (rsq < cut_ljsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - - fforce = forcecoul + factor_lj*forcelj; - - double eng = 0.0; - if (rsq < cut_coulsq) { - prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; - phicoul = prefactor*erfc; - if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; - eng += phicoul; - } - - if (rsq < cut_ljsq[itype][jtype]) { - philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - eng += factor_lj*philj; - } - - return eng; -} - -/* ---------------------------------------------------------------------- */ - -void *PairLJCutCoulLongSoft::extract(const char *str, int &dim) -{ - dim = 0; - if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; - dim = 2; - if (strcmp(str,"epsilon") == 0) return (void *) epsilon; - if (strcmp(str,"sigma") == 0) return (void *) sigma; - if (strcmp(str,"lambda") == 0) return (void *) lambda; - return NULL; -} +/* ---------------------------------------------------------------------- + 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: Paul Crozier (SNL) + Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_cut_coul_long_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulLongSoft::PairLJCutCoulLongSoft(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + respa_enable = 1; + writedata = 1; + qdist = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCutCoulLongSoft::~PairLJCutCoulLongSoft() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::compute(int eflag, int vflag) +{ + int i,ii,j,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; + double grij,expm2,prefactor,t,erfc; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + 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]; + 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]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + + fpair = forcecoul + factor_lj*forcelj; + + 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) { + if (rsq < cut_coulsq) { + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + ecoul = prefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::compute_inner() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcecoul,forcelj,factor_coul,factor_lj; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listinner->inum; + ilist = listinner->ilist; + numneigh = listinner->numneigh; + firstneigh = listinner->firstneigh; + + 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]; + qtmp = q[i]; + 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)]; + 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; + + if (rsq < cut_out_off_sq) { + jtype = type[j]; + + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + + fpair = forcecoul + factor_lj*forcelj; + + 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 PairLJCutCoulLongSoft::compute_middle() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcecoul,forcelj,factor_coul,factor_lj; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listmiddle->inum; + ilist = listmiddle->ilist; + numneigh = listmiddle->numneigh; + firstneigh = listmiddle->firstneigh; + + 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]; + qtmp = q[i]; + 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)]; + 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; + + if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) { + jtype = type[j]; + + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + + fpair = forcecoul + factor_lj*forcelj; + + 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 PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,forcecoul,forcelj,factor_coul,factor_lj; + double grij,expm2,fprefactor,eprefactor,t,erfc; + double rsw; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = listouter->inum; + ilist = listouter->ilist; + numneigh = listouter->numneigh; + firstneigh = listouter->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]; + qtmp = q[i]; + 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)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + + forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2 - 1.0); + + if (rsq > cut_in_off_sq) { + if (rsq < cut_in_on_sq) { + rsw = (r - cut_in_off)/cut_in_diff; + forcecoul += fprefactor*rsw*rsw*(3.0 - 2.0*rsw); + if (factor_coul < 1.0) + forcecoul -= + (1.0-factor_coul)*fprefactor*rsw*rsw*(3.0 - 2.0*rsw); + } else { + forcecoul += fprefactor; + if (factor_coul < 1.0) + forcecoul -= (1.0-factor_coul)*fprefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + if (rsq < cut_in_on_sq) { + rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff; + forcelj *= rsw*rsw*(3.0 - 2.0*rsw); + } + } else forcelj = 0.0; + + fpair = forcecoul + forcelj; + + 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) { + if (rsq < cut_coulsq) { + eprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + ecoul = eprefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*eprefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (vflag) { + if (rsq < cut_coulsq) { + forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*fprefactor; + } else forcecoul = 0.0; + + if (rsq <= cut_in_off_sq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else if (rsq < cut_in_on_sq) { + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } + fpair = forcecoul + factor_lj*forcelj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::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_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(lambda,n+1,n+1,"pair:lambda"); + 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 PairLJCutCoulLongSoft::settings(int narg, char **arg) +{ + if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + alphac = force->numeric(FLERR,arg[2]); + + cut_lj_global = force->numeric(FLERR,arg[3]); + if (narg == 4) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[4]); + + // reset cutoffs that have been explicitly set + + 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; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + 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(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + + double cut_lj_one = cut_lj_global; + if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]); + + 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; + lambda[i][j] = lambda_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style lj/cut/coul/long/soft requires atom attribute q"); + + // request regular or rRESPA neighbor lists + + int irequest; + + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + int respa = 0; + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + + if (respa == 0) irequest = neighbor->request(this,instance_me); + else if (respa == 1) { + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } else { + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 2; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respamiddle = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } + + } else irequest = neighbor->request(this,instance_me); + + cut_coulsq = cut_coul * cut_coul; + + // 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; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + regular or rRESPA +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::init_list(int id, NeighList *ptr) +{ + if (id == 0) list = ptr; + else if (id == 1) listinner = ptr; + else if (id == 2) listmiddle = ptr; + else if (id == 3) listouter = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCutCoulLongSoft::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]); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/cut/coul/long/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + 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] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag) { + double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); + offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + 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 interior rRESPA cutoff + + if (cut_respa && MIN(cut_lj[i][j],cut_coul) < 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 sig2 = sigma[i][j]*sigma[i][j]; + double sig6 = sig2*sig2*sig2; + double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + double rc6 = rc3*rc3; + double rc9 = rc3*rc6; + etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); + ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::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(&lambda[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(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&alphac,sizeof(double),1,fp); + + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&alphac,sizeof(double),1,fp); + + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,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(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); + + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJCutCoulLongSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCutCoulLongSoft::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r,grij,expm2,t,erfc,prefactor; + double forcecoul,forcelj,phicoul,philj; + double denc, denlj, r4sig6; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / + (denc*denc*denc); + + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + + fforce = forcecoul + factor_lj*forcelj; + + double eng = 0.0; + if (rsq < cut_coulsq) { + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; + phicoul = prefactor*erfc; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + + if (rsq < cut_ljsq[itype][jtype]) { + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + eng += factor_lj*philj; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJCutCoulLongSoft::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + return NULL; +} diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index f78f91e988..5f3a9cb6c6 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -1,779 +1,779 @@ -/* ---------------------------------------------------------------------- - 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: Paul Crozier (SNL) - Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "pair_lj_cut_soft.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; - -/* ---------------------------------------------------------------------- */ - -PairLJCutSoft::PairLJCutSoft(LAMMPS *lmp) : Pair(lmp) -{ - respa_enable = 1; - writedata = 1; - allocated = 0; -} - -/* ---------------------------------------------------------------------- */ - -PairLJCutSoft::~PairLJCutSoft() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lambda); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(offset); - allocated=0; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairLJCutSoft::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,forcelj,factor_lj; - double denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - 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]) { - - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - - fpair = factor_lj*forcelj; - - 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 = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - 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 PairLJCutSoft::compute_inner() -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,fpair; - double rsq,forcelj,factor_lj,rsw; - double denlj, r4sig6; - 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 = listinner->inum; - ilist = listinner->ilist; - numneigh = listinner->numneigh; - firstneigh = listinner->firstneigh; - - 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) { - jtype = type[j]; - - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - - fpair = factor_lj*forcelj; - - 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 PairLJCutSoft::compute_middle() -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,fpair; - double rsq,forcelj,factor_lj,rsw; - double denlj, r4sig6; - 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 = listmiddle->inum; - ilist = listmiddle->ilist; - numneigh = listmiddle->numneigh; - firstneigh = listmiddle->firstneigh; - - 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) { - jtype = type[j]; - - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - - fpair = factor_lj*forcelj; - - 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 PairLJCutSoft::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,forcelj,factor_lj,rsw; - double denlj, r4sig6; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; - - 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 = listouter->inum; - ilist = listouter->ilist; - numneigh = listouter->numneigh; - firstneigh = listouter->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) { - - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - - fpair = factor_lj*forcelj; - - 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) { - evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - evdwl *= factor_lj; - } - - if (vflag) { - if (rsq <= cut_in_off_sq) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - fpair = factor_lj*forcelj; - } else if (rsq < cut_in_on_sq) - fpair = factor_lj*forcelj; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - } -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairLJCutSoft::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(lambda,n+1,n+1,"pair:lambda"); - 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(offset,n+1,n+1,"pair:offset"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairLJCutSoft::settings(int narg, char **arg) -{ - if (narg != 3) error->all(FLERR,"Illegal pair_style command"); - - nlambda = force->numeric(FLERR,arg[0]); - alphalj = force->numeric(FLERR,arg[1]); - - cut_global = force->numeric(FLERR,arg[2]); - - // reset cutoffs that have been explicitly set - - 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[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairLJCutSoft::coeff(int narg, char **arg) -{ - if (narg < 5 || narg > 6) - error->all(FLERR,"Incorrect args for pair coefficients"); - 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(FLERR,arg[2]); - double sigma_one = force->numeric(FLERR,arg[3]); - double lambda_one = force->numeric(FLERR,arg[4]); - - double cut_one = cut_global; - if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); - - 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; - lambda[i][j] = lambda_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 PairLJCutSoft::init_style() -{ - // request regular or rRESPA neighbor lists - - int irequest; - - if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { - int respa = 0; - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; - - if (respa == 0) irequest = neighbor->request(this,instance_me); - else if (respa == 1) { - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respainner = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 3; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respaouter = 1; - } else { - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respainner = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 2; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respamiddle = 1; - irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->id = 3; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->respaouter = 1; - } - - } else irequest = neighbor->request(this,instance_me); - - // 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; - -} - -/* ---------------------------------------------------------------------- - neighbor callback to inform pair style of neighbor list to use - regular or rRESPA -------------------------------------------------------------------------- */ - -void PairLJCutSoft::init_list(int id, NeighList *ptr) -{ - if (id == 0) list = ptr; - else if (id == 1) listinner = ptr; - else if (id == 2) listmiddle = ptr; - else if (id == 3) listouter = ptr; -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairLJCutSoft::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[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - lj1[i][j] = pow(lambda[i][j], nlambda); - lj2[i][j] = pow(sigma[i][j], 6.0); - lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); - - if (offset_flag) { - double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0); - offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); - } else offset[i][j] = 0.0; - - epsilon[j][i] = epsilon[i][j]; - sigma[j][i] = sigma[i][j]; - lambda[j][i] = lambda[i][j]; - lj1[j][i] = lj1[i][j]; - lj2[j][i] = lj2[i][j]; - lj3[j][i] = lj3[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 sig2 = sigma[i][j]*sigma[i][j]; - double sig6 = sig2*sig2*sig2; - double rc3 = cut[i][j]*cut[i][j]*cut[i][j]; - double rc6 = rc3*rc3; - double rc9 = rc3*rc6; - etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); - ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * - sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); - } - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutSoft::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(&lambda[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJCutSoft::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(&lambda[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(&lambda[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJCutSoft::write_restart_settings(FILE *fp) -{ - fwrite(&nlambda,sizeof(double),1,fp); - fwrite(&alphalj,sizeof(double),1,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 PairLJCutSoft::read_restart_settings(FILE *fp) -{ - int me = comm->me; - if (me == 0) { - fread(&nlambda,sizeof(double),1,fp); - fread(&alphalj,sizeof(double),1,fp); - - 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(&nlambda,1,MPI_DOUBLE,0,world); - MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); - - 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 PairLJCutSoft::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairLJCutSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], - lambda[i][j],cut[i][j]); -} - -/* ---------------------------------------------------------------------- */ - -double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double forcelj,philj; - double r4sig6, denlj; - - if (rsq < cutsq[itype][jtype]) { - r4sig6 = rsq*rsq / lj2[itype][jtype]; - denlj = lj3[itype][jtype] + rsq*r4sig6; - forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * - (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); - } else forcelj = 0.0; - fforce = factor_lj*forcelj; - - if (rsq < cutsq[itype][jtype]) { - philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * - (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; - } else philj = 0.0; - - return factor_lj*philj; -} - -/* ---------------------------------------------------------------------- */ - -void *PairLJCutSoft::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,"lambda") == 0) return (void *) lambda; - return NULL; -} +/* ---------------------------------------------------------------------- + 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: Paul Crozier (SNL) + Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_lj_cut_soft.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; + +/* ---------------------------------------------------------------------- */ + +PairLJCutSoft::PairLJCutSoft(LAMMPS *lmp) : Pair(lmp) +{ + respa_enable = 1; + writedata = 1; + allocated = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairLJCutSoft::~PairLJCutSoft() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(offset); + allocated=0; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJCutSoft::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,forcelj,factor_lj; + double denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + 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]) { + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + fpair = factor_lj*forcelj; + + 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 = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - 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 PairLJCutSoft::compute_inner() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcelj,factor_lj,rsw; + double denlj, r4sig6; + 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 = listinner->inum; + ilist = listinner->ilist; + numneigh = listinner->numneigh; + firstneigh = listinner->firstneigh; + + 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) { + jtype = type[j]; + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + fpair = factor_lj*forcelj; + + 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 PairLJCutSoft::compute_middle() +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,fpair; + double rsq,forcelj,factor_lj,rsw; + double denlj, r4sig6; + 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 = listmiddle->inum; + ilist = listmiddle->ilist; + numneigh = listmiddle->numneigh; + firstneigh = listmiddle->firstneigh; + + 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) { + jtype = type[j]; + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + fpair = factor_lj*forcelj; + + 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 PairLJCutSoft::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,forcelj,factor_lj,rsw; + double denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + 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 = listouter->inum; + ilist = listouter->ilist; + numneigh = listouter->numneigh; + firstneigh = listouter->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) { + + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + + fpair = factor_lj*forcelj; + + 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) { + evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (vflag) { + if (rsq <= cut_in_off_sq) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + fpair = factor_lj*forcelj; + } else if (rsq < cut_in_on_sq) + fpair = factor_lj*forcelj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJCutSoft::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(lambda,n+1,n+1,"pair:lambda"); + 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(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJCutSoft::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + + cut_global = force->numeric(FLERR,arg[2]); + + // reset cutoffs that have been explicitly set + + 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[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJCutSoft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + 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(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + + double cut_one = cut_global; + if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); + + 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; + lambda[i][j] = lambda_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 PairLJCutSoft::init_style() +{ + // request regular or rRESPA neighbor lists + + int irequest; + + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + int respa = 0; + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + + if (respa == 0) irequest = neighbor->request(this,instance_me); + else if (respa == 1) { + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } else { + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respainner = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 2; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respamiddle = 1; + irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = 3; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->respaouter = 1; + } + + } else irequest = neighbor->request(this,instance_me); + + // 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; + +} + +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + regular or rRESPA +------------------------------------------------------------------------- */ + +void PairLJCutSoft::init_list(int id, NeighList *ptr) +{ + if (id == 0) list = ptr; + else if (id == 1) listinner = ptr; + else if (id == 2) listmiddle = ptr; + else if (id == 3) listouter = ptr; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJCutSoft::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[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag) { + double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0); + offset[i][j] = lj1[i][j] * 4.0 * epsilon[i][j] * (1.0/(denlj*denlj) - 1.0/denlj); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[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 sig2 = sigma[i][j]*sigma[i][j]; + double sig6 = sig2*sig2*sig2; + double rc3 = cut[i][j]*cut[i][j]*cut[i][j]; + double rc6 = rc3*rc3; + double rc9 = rc3*rc6; + etail_ij = 8.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (sig6 - 3.0*rc6) / (9.0*rc9); + ptail_ij = 16.0*MY_PI*all[0]*all[1]* lj1[i][j] * epsilon[i][j] * + sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9); + } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutSoft::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(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJCutSoft::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(&lambda[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(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJCutSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,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 PairLJCutSoft::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + + 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(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + + 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 PairLJCutSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJCutSoft::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 %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJCutSoft::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double forcelj,philj; + double r4sig6, denlj; + + if (rsq < cutsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + fforce = factor_lj*forcelj; + + if (rsq < cutsq[itype][jtype]) { + philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] * + (1.0/(denlj*denlj) - 1.0/denlj) - offset[itype][jtype]; + } else philj = 0.0; + + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJCutSoft::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,"lambda") == 0) return (void *) lambda; + return NULL; +}