diff --git a/src/pair_zhou.cpp b/src/pair_zhou.cpp deleted file mode 100644 index fc5569574c..0000000000 --- a/src/pair_zhou.cpp +++ /dev/null @@ -1,361 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include "math.h" -#include "stdio.h" -#include "stdlib.h" -#include "pair_zhou.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -PairZhou::PairZhou(LAMMPS *lmp) : Pair(lmp) {} - -/* ---------------------------------------------------------------------- */ - -PairZhou::~PairZhou() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut); - memory->destroy(d0); - memory->destroy(alpha); - memory->destroy(r0); - memory->destroy(c); - memory->destroy(rr); - memory->destroy(morse1); - memory->destroy(offset); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairZhou::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,r,dr,dexp,factor_lj,r2inv,r6inv,ddexp,invexp; - 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]) { - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - r = sqrt(rsq); - dr = r - r0[itype][jtype]; - dexp = exp(-alpha[itype][jtype] * dr); - ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0)); - invexp = 1.0/(1+ddexp); - fpair = morse1[itype][jtype] * (dexp*dexp - dexp) / r; - fpair -= sscale*c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r; - fpair -= sscale*c[itype][jtype] * (6.0 * invexp * r6inv * r2inv); - fpair *= factor_lj; - - 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 = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - - sscale*c[itype][jtype]*r6inv*invexp - 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(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairZhou::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(d0,n+1,n+1,"pair:d0"); - memory->create(alpha,n+1,n+1,"pair:alpha"); - memory->create(r0,n+1,n+1,"pair:r0"); - memory->create(c,n+1,n+1,"pair:c"); - memory->create(rr,n+1,n+1,"pair:rr"); - memory->create(morse1,n+1,n+1,"pair:morse1"); - memory->create(offset,n+1,n+1,"pair:offset"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairZhou::settings(int narg, char **arg) -{ - if (narg != 3) error->all(FLERR,"Illegal pair_style command"); - - cut_global = force->numeric(FLERR,arg[0]); - sscale = force->numeric(FLERR,arg[1]); - dscale = 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 PairZhou::coeff(int narg, char **arg) -{ - if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - double d0_one = force->numeric(FLERR,arg[2]); - double alpha_one = force->numeric(FLERR,arg[3]); - double r0_one = force->numeric(FLERR,arg[4]); - double c_one = force->numeric(FLERR,arg[5]); - double rr_one = force->numeric(FLERR,arg[6]); - - double cut_one = cut_global; - if (narg == 8) cut_one = force->numeric(FLERR,arg[7]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - d0[i][j] = d0_one; - alpha[i][j] = alpha_one; - r0[i][j] = r0_one; - cut[i][j] = cut_one; - c[i][j] = c_one; - rr[i][j] = rr_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairZhou::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; - - if (offset_flag) { - double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]); - offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr)); - } else offset[i][j] = 0.0; - - d0[j][i] = d0[i][j]; - alpha[j][i] = alpha[i][j]; - r0[j][i] = r0[i][j]; - c[j][i] = c[i][j]; - rr[j][i] = rr[i][j]; - morse1[j][i] = morse1[i][j]; - offset[j][i] = offset[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairZhou::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(&d0[i][j],sizeof(double),1,fp); - fwrite(&alpha[i][j],sizeof(double),1,fp); - fwrite(&r0[i][j],sizeof(double),1,fp); - fwrite(&c[i][j],sizeof(double),1,fp); - fwrite(&rr[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairZhou::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(&d0[i][j],sizeof(double),1,fp); - fread(&alpha[i][j],sizeof(double),1,fp); - fread(&r0[i][j],sizeof(double),1,fp); - fread(&c[i][j],sizeof(double),1,fp); - fread(&rr[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - } - MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&rr[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairZhou::write_restart_settings(FILE *fp) -{ - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&sscale,sizeof(double),1,fp); - fwrite(&dscale,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairZhou::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - fread(&cut_global,sizeof(double),1,fp); - fread(&sscale,sizeof(double),1,fp); - fread(&dscale,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&sscale,1,MPI_DOUBLE,0,world); - MPI_Bcast(&dscale,1,MPI_DOUBLE,0,world); - MPI_Bcast(&offset_flag,1,MPI_INT,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- */ - -double PairZhou::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp; - - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - r = sqrt(rsq); - dr = r - r0[itype][jtype]; - dexp = exp(-alpha[itype][jtype] * dr); - ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0)); - invexp = 1.0/(1+ddexp); - fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r; - fforce -= factor_lj * sscale* c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r; - fforce -= factor_lj * sscale* c[itype][jtype] * (6.0 * invexp * r6inv * r2inv); - - phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype]; - return factor_lj*phi; -} - diff --git a/src/pair_zhou.h b/src/pair_zhou.h deleted file mode 100644 index e8a4effa78..0000000000 --- a/src/pair_zhou.h +++ /dev/null @@ -1,75 +0,0 @@ -/* ---------------------------------------------------------------------- - 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. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(zhou,PairZhou) - -#else - -#ifndef LMP_PAIR_ZHOU_H -#define LMP_PAIR_ZHOU_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairZhou : public Pair { - public: - PairZhou(class LAMMPS *); - virtual ~PairZhou(); - - virtual void compute(int, int); - virtual void settings(int, char **); - void coeff(int, char **); - virtual double init_one(int, int); - void write_restart(FILE *); - void read_restart(FILE *); - void write_restart_settings(FILE *); - void read_restart_settings(FILE *); - virtual double single(int, int, int, int, double, double, double, double &); - - protected: - double cut_global; - double **cut; - double sscale,dscale; - double **d0,**alpha,**r0,**c,**rr; - double **morse1; - double **offset; - - void allocate(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: All pair coeffs are not set - -All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. - -*/