diff --git a/src/.gitignore b/src/.gitignore index 632b46a08a..02b05b364b 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -976,6 +976,8 @@ /fix_ttm_mod.h /pair_born_coul_long_cs.cpp /pair_born_coul_long_cs.h +/pair_born_coul_dsf_cs.cpp +/pair_born_coul_dsf_cs.h /pair_buck_coul_long_cs.cpp /pair_buck_coul_long_cs.h /pair_coul_long_cs.cpp diff --git a/src/CORESHELL/Install.sh b/src/CORESHELL/Install.sh index f5ea54ac86..7c0b7a02a2 100644 --- a/src/CORESHELL/Install.sh +++ b/src/CORESHELL/Install.sh @@ -31,8 +31,10 @@ action () { action compute_temp_cs.cpp action compute_temp_cs.h action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp +action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp action pair_born_coul_long_cs.h pair_born_coul_long.h +action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h action pair_buck_coul_long_cs.h pair_buck_coul_long.h action pair_coul_long_cs.cpp pair_coul_long.cpp action pair_coul_long_cs.h pair_coul_long.h diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp new file mode 100644 index 0000000000..2cd2f211ff --- /dev/null +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -0,0 +1,162 @@ +/* ---------------------------------------------------------------------- + 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: Ariel Lozano (arielzn@gmail.com) + References: Fennell and Gezelter, JCP 124, 234104 (2006) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_born_coul_dsf_cs.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" +#include "math_special.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EPSILON 1.0e-20 + + +/* ---------------------------------------------------------------------- */ + +PairBornCoulDSFCS::PairBornCoulDSFCS(LAMMPS *lmp) : PairBornCoulDSF(lmp) +{ + writedata = 1; + single_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulDSFCS::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 r,rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double prefactor,erfcc,erfcd,arg; + double rexp; + 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_lj = force->special_lj; + double *special_coul = force->special_coul; + 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]; + + // self coulombic energy + if (eflag) { + double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e; + ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0); + } + + 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]) { + rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond; + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = qqrd2e*qtmp*q[j] / r; + arg = alpha * r ; + erfcd = MathSpecial::expmsq(arg); + erfcc = MathSpecial::my_erfcx(arg) * erfcd; + forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd + + r*f_shift) * r; + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = (forcecoul + factor_lj*forceborn) * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift); + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - 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(); +} + diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.h b/src/CORESHELL/pair_born_coul_dsf_cs.h new file mode 100644 index 0000000000..a49df5971c --- /dev/null +++ b/src/CORESHELL/pair_born_coul_dsf_cs.h @@ -0,0 +1,59 @@ +/* -*- 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(born/coul/dsf/cs,PairBornCoulDSFCS) + +#else + +#ifndef LMP_PAIR_BORN_COUL_DSF_CS_H +#define LMP_PAIR_BORN_COUL_DSF_CS_H + +#include "pair_born_coul_dsf.h" + +namespace LAMMPS_NS { + +class PairBornCoulDSFCS : public PairBornCoulDSF { + public: + PairBornCoulDSFCS(class LAMMPS *); + virtual void compute(int, int); +}; + +} + +#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: Pair style born/coul/dsf requires atom attribute q + +The atom style defined does not have this attribute. + +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. + +*/ diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp new file mode 100644 index 0000000000..eb3b817410 --- /dev/null +++ b/src/pair_born_coul_dsf.cpp @@ -0,0 +1,494 @@ +/* ---------------------------------------------------------------------- + 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: Ariel Lozano (arielzn@gmail.com) + References: Fennell and Gezelter, JCP 124, 234104 (2006) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_born_coul_dsf.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" +#include "math_special.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairBornCoulDSF::PairBornCoulDSF(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; + single_enable = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairBornCoulDSF::~PairBornCoulDSF() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(a); + memory->destroy(rho); + memory->destroy(sigma); + memory->destroy(c); + memory->destroy(d); + memory->destroy(rhoinv); + memory->destroy(born1); + memory->destroy(born2); + memory->destroy(born3); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulDSF::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 r,rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double prefactor,erfcc,erfcd,arg; + double rexp; + 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_lj = force->special_lj; + double *special_coul = force->special_coul; + 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]; + + // self coulombic energy + if (eflag) { + double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e; + ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0); + } + + 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]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = qqrd2e*qtmp*q[j]/r; + arg = alpha * r ; + erfcd = MathSpecial::expmsq(arg); + erfcc = MathSpecial::my_erfcx(arg) * erfcd; + forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd + + r*f_shift) * r; + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = (forcecoul + factor_lj*forceborn) * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift); + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - 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 PairBornCoulDSF::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(a,n+1,n+1,"pair:a"); + memory->create(rho,n+1,n+1,"pair:rho"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(c,n+1,n+1,"pair:c"); + memory->create(d,n+1,n+1,"pair:d"); + memory->create(rhoinv,n+1,n+1,"pair:rhoinv"); + memory->create(born1,n+1,n+1,"pair:born1"); + memory->create(born2,n+1,n+1,"pair:born2"); + memory->create(born3,n+1,n+1,"pair:born3"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::settings(int narg, char **arg) +{ + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + + alpha = force->numeric(FLERR,arg[0]); + cut_lj_global = force->numeric(FLERR,arg[1]); + if (narg == 2) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[2]); + + 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 PairBornCoulDSF::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 a_one = force->numeric(FLERR,arg[2]); + double rho_one = force->numeric(FLERR,arg[3]); + double sigma_one = force->numeric(FLERR,arg[4]); + if (rho_one <= 0) error->all(FLERR,"Incorrect args for pair coefficients"); + double c_one = force->numeric(FLERR,arg[5]); + double d_one = force->numeric(FLERR,arg[6]); + + double cut_lj_one = cut_lj_global; + if (narg == 8) cut_lj_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++) { + a[i][j] = a_one; + rho[i][j] = rho_one; + sigma[i][j] = sigma_one; + c[i][j] = c_one; + d[i][j] = d_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 PairBornCoulDSF::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style born/coul/dsf requires atom attribute q"); + + neighbor->request(this,instance_me); + + cut_coulsq = cut_coul * cut_coul; + double erfcc = erfc(alpha*cut_coul); + double erfcd = exp(-alpha*alpha*cut_coul*cut_coul); + f_shift = -(erfcc/cut_coulsq + 2.0/MY_PIS*alpha*erfcd/cut_coul); + e_shift = erfcc/cut_coul - f_shift*cut_coul; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBornCoulDSF::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + rhoinv[i][j] = 1.0/rho[i][j]; + born1[i][j] = a[i][j]/rho[i][j]; + born2[i][j] = 6.0*c[i][j]; + born3[i][j] = 8.0*d[i][j]; + + if (offset_flag) { + double rexp = exp((sigma[i][j]-cut_lj[i][j])*rhoinv[i][j]); + offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0) + + d[i][j]/pow(cut_lj[i][j],8.0); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + a[j][i] = a[i][j]; + c[j][i] = c[i][j]; + d[j][i] = d[i][j]; + rhoinv[j][i] = rhoinv[i][j]; + sigma[j][i] = sigma[i][j]; + born1[j][i] = born1[i][j]; + born2[j][i] = born2[i][j]; + born3[j][i] = born3[i][j]; + offset[j][i] = offset[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::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(&a[i][j],sizeof(double),1,fp); + fwrite(&rho[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&c[i][j],sizeof(double),1,fp); + fwrite(&d[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::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(&a[i][j],sizeof(double),1,fp); + fread(&rho[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&c[i][j],sizeof(double),1,fp); + fread(&d[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&d[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 PairBornCoulDSF::write_restart_settings(FILE *fp) +{ + fwrite(&alpha,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); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&alpha,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); + } + MPI_Bcast(&alpha,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); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i, + a[i][i],rho[i][i],sigma[i][i],c[i][i],d[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairBornCoulDSF::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 %g %g\n",i,j, + a[i][j],rho[i][j],sigma[i][j],c[i][j],d[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- + only the pair part is calculated here +------------------------------------------------------------------------- */ + +double PairBornCoulDSF::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,prefactor,rexp; + double forcecoul,forceborn,phicoul,phiborn; + double erfcc,erfcd,arg; + + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = factor_coul * force->qqrd2e * atom->q[i]*atom->q[j]/r; + + arg = alpha * r ; + erfcd = MathSpecial::expmsq(arg); + erfcc = MathSpecial::my_erfcx(arg) * erfcd; + + forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS*erfcd + + r*f_shift) * r; + + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp(-r*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fforce = (forcecoul + factor_lj*forceborn) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq) { + phicoul = prefactor * (erfcc - r*e_shift - rsq*f_shift); + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r2inv*r6inv - offset[itype][jtype]; + eng += factor_lj*phiborn; + } + return eng; +} diff --git a/src/pair_born_coul_dsf.h b/src/pair_born_coul_dsf.h new file mode 100644 index 0000000000..c7cfb26094 --- /dev/null +++ b/src/pair_born_coul_dsf.h @@ -0,0 +1,81 @@ +/* -*- 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(born/coul/dsf,PairBornCoulDSF) + +#else + +#ifndef LMP_PAIR_BORN_COUL_DSF_H +#define LMP_PAIR_BORN_COUL_DSF_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBornCoulDSF : public Pair { + public: + PairBornCoulDSF(class LAMMPS *); + virtual ~PairBornCoulDSF(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_lj_global,alpha; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **a,**rho,**sigma,**c,**d; + double **rhoinv,**born1,**born2,**born3,**offset; + double f_shift,e_shift; + + 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: Pair style born/coul/dsf requires atom attribute q + +The atom style defined does not have this attribute. + +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. + +*/