diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 52ee6cad94..fdd2c9b096 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -69,4 +69,5 @@ pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16 pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14 pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11 +pair_style zhou, Kristen Fichthorn, fichthorn@psu.edu, 18 Mar 17 temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16 diff --git a/src/USER-MISC/pair_zhou.cpp b/src/USER-MISC/pair_zhou.cpp new file mode 100644 index 0000000000..fc5569574c --- /dev/null +++ b/src/USER-MISC/pair_zhou.cpp @@ -0,0 +1,361 @@ +/* ---------------------------------------------------------------------- + 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/USER-MISC/pair_zhou.h b/src/USER-MISC/pair_zhou.h new file mode 100644 index 0000000000..e8a4effa78 --- /dev/null +++ b/src/USER-MISC/pair_zhou.h @@ -0,0 +1,75 @@ +/* ---------------------------------------------------------------------- + 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. + +*/