diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp new file mode 100644 index 0000000000..443de0cccf --- /dev/null +++ b/src/pair_beck.cpp @@ -0,0 +1,362 @@ +/* ---------------------------------------------------------------------- + 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: Jonathan Zimmerman (Sandia) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "pair_beck.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairBeck::PairBeck(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairBeck::~PairBeck() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(AA); + memory->destroy(BB); + memory->destroy(aa); + memory->destroy(alpha); + memory->destroy(beta); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBeck::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,r5,force_beck,factor_lj; + double r,rinv; + double aaij,alphaij,betaij; + double term1,term1inv,term2,term3,term4,term5,term6; + 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]) { + r = sqrt(rsq); + r5 = rsq*rsq*r; + aaij = aa[itype][jtype]; + alphaij = alpha[itype][jtype]; + betaij = beta[itype][jtype]; + term1 = aaij*aaij + rsq; + term2 = 1.0/pow(term1,5); + term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq; + term4 = alphaij + r5*betaij; + term5 = alphaij + 6.0*r5*betaij; + rinv = 1.0/r; + force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5; + force_beck -= BB[itype][jtype]*r*term2*term3; + + fpair = factor_lj*force_beck*rinv; + + 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) { + term6 = 1.0/pow(term1,3); + term1inv = 1.0/term1; + evdwl = AA[itype][jtype]*exp(-1.0*r*term4); + evdwl -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv); + } + + 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 PairBeck::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(AA,n+1,n+1,"pair:AA"); + memory->create(BB,n+1,n+1,"pair:BB"); + memory->create(aa,n+1,n+1,"pair:aa"); + memory->create(alpha,n+1,n+1,"pair:alpha"); + memory->create(beta,n+1,n+1,"pair:beta"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBeck::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = atof(arg[0]); + + // 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 PairBeck::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(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double AA_one = atof(arg[2]); + double BB_one = atof(arg[3]); + double aa_one = atof(arg[4]); + double alpha_one = atof(arg[5]); + double beta_one = atof(arg[6]); + + double cut_one = cut_global; + if (narg == 8) cut_one = atof(arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + AA[i][j] = AA_one; + BB[i][j] = BB_one; + aa[i][j] = aa_one; + alpha[i][j] = alpha_one; + beta[i][j] = beta_one; + cut[i][j] = cut_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 PairBeck::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + AA[j][i] = AA[i][j]; + BB[j][i] = BB[i][j]; + aa[j][i] = aa[i][j]; + alpha[j][i] = alpha[i][j]; + beta[j][i] = beta[i][j]; + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBeck::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(&AA[i][j],sizeof(double),1,fp); + fwrite(&BB[i][j],sizeof(double),1,fp); + fwrite(&aa[i][j],sizeof(double),1,fp); + fwrite(&alpha[i][j],sizeof(double),1,fp); + fwrite(&beta[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBeck::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(&AA[i][j],sizeof(double),1,fp); + fread(&BB[i][j],sizeof(double),1,fp); + fread(&aa[i][j],sizeof(double),1,fp); + fread(&alpha[i][j],sizeof(double),1,fp); + fread(&beta[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&AA[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&BB[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&aa[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBeck::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBeck::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairBeck::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double phi_beck,r,rinv; + double r5,force_beck; + double aaij,alphaij,betaij; + double term1,term1inv,term2,term3,term4,term5,term6; + + r = sqrt(rsq); + r5 = rsq*rsq*r; + aaij = aa[itype][jtype]; + alphaij = alpha[itype][jtype]; + betaij = beta[itype][jtype]; + term1 = aaij*aaij + rsq; + term2 = 1.0/pow(term1,5); + term3 = 21.672 + 30.0*aaij*aaij + 6.0*rsq; + term4 = alphaij + r5*betaij; + term5 = alphaij + 6.0*r5*betaij; + rinv = 1.0/r; + force_beck = AA[itype][jtype]*exp(-1.0*r*term4)*term5; + force_beck -= BB[itype][jtype]*r*term2*term3; + fforce = factor_lj*force_beck*rinv; + + term6 = 1.0/pow(term1,3); + term1inv = 1.0/term1; + phi_beck = AA[itype][jtype]*exp(-1.0*r*term4); + phi_beck -= BB[itype][jtype]*term6*(1.0+(2.709+3.0*aaij*aaij)*term1inv); + + return factor_lj*phi_beck; +} diff --git a/src/pair_beck.h b/src/pair_beck.h new file mode 100644 index 0000000000..4a4147b067 --- /dev/null +++ b/src/pair_beck.h @@ -0,0 +1,53 @@ +/* -*- c++ -*- ---------------------------------------------------------- + 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(beck,PairBeck) + +#else + +#ifndef PAIR_BECK_H +#define PAIR_BECK_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBeck : public Pair { + public: + PairBeck(class LAMMPS *); + virtual ~PairBeck(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global; + double **cut; + double **AA,**BB; + double **aa,**alpha,**beta; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 0e544c116e..f631fc4416 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -170,7 +170,8 @@ void PairYukawa::settings(int narg, char **arg) void PairYukawa::coeff(int narg, char **arg) { - if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 3 || narg > 4) + error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); int ilo,ihi,jlo,jhi;