From 270d94c5ef7725745d28135ba4590e5cad570e2e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 30 Aug 2013 23:04:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10700 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/MISC/pair_nm_cut.cpp | 433 +++++++++++++++++++++ src/MISC/pair_nm_cut.h | 57 +++ src/MISC/pair_nm_cut_coul_cut.cpp | 506 +++++++++++++++++++++++++ src/MISC/pair_nm_cut_coul_cut.h | 78 ++++ src/MISC/pair_nm_cut_coul_long.cpp | 590 +++++++++++++++++++++++++++++ src/MISC/pair_nm_cut_coul_long.h | 84 ++++ 6 files changed, 1748 insertions(+) create mode 100644 src/MISC/pair_nm_cut.cpp create mode 100644 src/MISC/pair_nm_cut.h create mode 100644 src/MISC/pair_nm_cut_coul_cut.cpp create mode 100644 src/MISC/pair_nm_cut_coul_cut.h create mode 100644 src/MISC/pair_nm_cut_coul_long.cpp create mode 100644 src/MISC/pair_nm_cut_coul_long.h diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp new file mode 100644 index 0000000000..b8bbb57dfe --- /dev/null +++ b/src/MISC/pair_nm_cut.cpp @@ -0,0 +1,433 @@ +/* ---------------------------------------------------------------------- + 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: Julien Devemy (ICCF) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_nm_cut.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairNMCut::PairNMCut(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairNMCut::~PairNMCut() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(e0); + memory->destroy(r0); + memory->destroy(nn); + memory->destroy(mm); + memory->destroy(nm); + memory->destroy(e0nm); + memory->destroy(r0n); + memory->destroy(r0m); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairNMCut::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,r2inv,factor_lj; + double r,forcenm,rminv,rninv; + 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; + r = sqrt(rsq); + + rminv = pow(r2inv,mm[itype][jtype]/2.0); + rninv = pow(r2inv,nn[itype][jtype]/2.0); + + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + fpair = factor_lj*forcenm*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) { + evdwl = e0nm[itype][jtype] * + (mm[itype][jtype]*r0n[itype][jtype]*rninv - + nn[itype][jtype]*r0m[itype][jtype]*rminv) - 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 PairNMCut::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(e0,n+1,n+1,"pair:e0"); + memory->create(r0,n+1,n+1,"pair:r0"); + memory->create(nn,n+1,n+1,"pair:nn"); + memory->create(mm,n+1,n+1,"pair:mm"); + memory->create(nm,n+1,n+1,"pair:nm"); + memory->create(e0nm,n+1,n+1,"pair:e0nm"); + memory->create(r0n,n+1,n+1,"pair:r0n"); + memory->create(r0m,n+1,n+1,"pair:r0m"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairNMCut::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = force->numeric(FLERR,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 PairNMCut::coeff(int narg, char **arg) +{ + if (narg < 6 || 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 e0_one = force->numeric(FLERR,arg[2]); + double r0_one = force->numeric(FLERR,arg[3]); + double nn_one = force->numeric(FLERR,arg[4]); + double mm_one = force->numeric(FLERR,arg[5]); + + double cut_one = cut_global; + if (narg == 7) cut_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++) { + e0[i][j] = e0_one; + r0[i][j] = r0_one; + nn[i][j] = nn_one; + mm[i][j] = mm_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 PairNMCut::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + nm[i][j] = nn[i][j]*mm[i][j]; + e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]); + r0n[i][j] = pow(r0[i][j],nn[i][j]); + r0m[i][j] = pow(r0[i][j],mm[i][j]); + + if (offset_flag) { + offset[i][j] = e0nm[i][j] * + ((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) - + (nn[i][j]*r0m[i][j] / pow(cut[i][j],mm[i][j]))); + } else offset[i][j] = 0.0; + + e0[j][i] = e0[i][j]; + nn[j][i] = nn[i][j]; + mm[j][i] = mm[i][j]; + nm[j][i] = nm[i][j]; + r0[j][i] = r0[i][j]; + e0nm[j][i] = e0nm[i][j]; + r0n[j][i] = r0n[i][j]; + r0m[j][i] = r0m[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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); + double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); + double p1 = 1-nn[i][j]; + double p2 = 1-mm[i][j]; + + double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); + double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); + + etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * + (rr1*pow(cut[i][j],p1)-rr2*pow(cut[i][j],p2)); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * + nn[i][j]*mm[i][j]*(rrr1*pow(cut[i][j],p1)-rrr2*pow(cut[i][j],p2)); + } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNMCut::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(&e0[i][j],sizeof(double),1,fp); + fwrite(&r0[i][j],sizeof(double),1,fp); + fwrite(&nn[i][j],sizeof(double),1,fp); + fwrite(&mm[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairNMCut::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(&e0[i][j],sizeof(double),1,fp); + fread(&r0[i][j],sizeof(double),1,fp); + fread(&nn[i][j],sizeof(double),1,fp); + fread(&mm[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&mm[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNMCut::write_restart_settings(FILE *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 PairNMCut::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + 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(&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 PairNMCut::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairNMCut::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\n",i,j, + e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairNMCut::single(int i, int j, int itype, int jtype, + double rsq, double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r,forcenm,phinm; + + r2inv = 1.0/rsq; + r = sqrt(rsq); + + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + fforce = factor_lj*forcenm*r2inv; + + phinm = e0nm[itype][jtype] * + (mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) - + offset[itype][jtype]; + return factor_lj*phinm; +} + +/* ---------------------------------------------------------------------- */ + +void *PairNMCut::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"e0") == 0) return (void *) e0; + if (strcmp(str,"r0") == 0) return (void *) r0; + if (strcmp(str,"nn") == 0) return (void *) nn; + if (strcmp(str,"mm") == 0) return (void *) mm; + return NULL; +} diff --git a/src/MISC/pair_nm_cut.h b/src/MISC/pair_nm_cut.h new file mode 100644 index 0000000000..2594eff3d8 --- /dev/null +++ b/src/MISC/pair_nm_cut.h @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + 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(nm/cut,PairNMCut) + +#else + +#ifndef LMP_PAIR_NM_CUT_H +#define LMP_PAIR_NM_CUT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairNMCut : public Pair { + public: + PairNMCut(class LAMMPS *); + virtual ~PairNMCut(); + + virtual 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 *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **cut; + double **e0,**r0,**nn, **mm; + double **nm,**e0nm,**r0n,**r0m,**offset; + + void allocate(); +}; + +} + +#endif +#endif diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp new file mode 100644 index 0000000000..6b1d6c5428 --- /dev/null +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -0,0 +1,506 @@ +/* ---------------------------------------------------------------------- + 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: Julien Devemy (ICCF) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_nm_cut_coul_cut.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; + +/* ---------------------------------------------------------------------- */ + +PairNMCutCoulCut::PairNMCutCoulCut(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairNMCutCoulCut::~PairNMCutCoulCut() +{ + 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(e0); + memory->destroy(r0); + memory->destroy(nn); + memory->destroy(mm); + memory->destroy(nm); + memory->destroy(e0nm); + memory->destroy(r0n); + memory->destroy(r0m); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairNMCutCoulCut::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,r2inv,factor_coul,factor_lj; + double r,forcecoul,forcenm,rminv,rninv; + 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]) { + r2inv = 1.0/rsq; + if (rsq < cut_coulsq[itype][jtype]) + forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv); + else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + rminv = pow(r2inv,mm[itype][jtype]/2.0); + rninv = pow(r2inv,nn[itype][jtype]/2.0); + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + } else forcenm = 0.0; + + fpair = (factor_coul*forcecoul + factor_lj*forcenm) * 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[itype][jtype]) + ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv); + else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = e0nm[itype][jtype]*(mm[itype][jtype] * + r0n[itype][jtype]*rninv - + nn[itype][jtype] * + r0m[itype][jtype]*rminv) - + 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 PairNMCutCoulCut::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(e0,n+1,n+1,"pair:e0"); + memory->create(r0,n+1,n+1,"pair:r0"); + memory->create(nn,n+1,n+1,"pair:nn"); + memory->create(mm,n+1,n+1,"pair:mm"); + memory->create(nm,n+1,n+1,"pair:nm"); + memory->create(e0nm,n+1,n+1,"pair:e0nm"); + memory->create(r0n,n+1,n+1,"pair:r0n"); + memory->create(r0m,n+1,n+1,"pair:r0m"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairNMCutCoulCut::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); + + cut_lj_global = force->numeric(FLERR,arg[0]); + if (narg == 1) cut_coul_global = cut_lj_global; + else cut_coul_global = force->numeric(FLERR,arg[1]); + + // 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 PairNMCutCoulCut::coeff(int narg, char **arg) +{ + if (narg < 6 || 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 e0_one = force->numeric(FLERR,arg[2]); + double r0_one = force->numeric(FLERR,arg[3]); + double nn_one = force->numeric(FLERR,arg[4]); + double mm_one = force->numeric(FLERR,arg[5]); + + double cut_lj_one = cut_lj_global; + double cut_coul_one = cut_coul_global; + if (narg >= 7) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[4]); + if (narg == 8) cut_coul_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++) { + e0[i][j] = e0_one; + r0[i][j] = r0_one; + nn[i][j] = nn_one; + mm[i][j] = mm_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 PairNMCutCoulCut::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style nm/cut/coul/cut requires atom attribute q"); + + neighbor->request(this); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairNMCutCoulCut::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[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]; + + nm[i][j] = nn[i][j]*mm[i][j]; + e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]); + r0n[i][j] = pow(r0[i][j],nn[i][j]); + r0m[i][j] = pow(r0[i][j],mm[i][j]); + + if (offset_flag) { + offset[i][j] = e0nm[i][j] * + ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) - + (nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j]))); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + cut_coulsq[j][i] = cut_coulsq[i][j]; + e0[j][i] = e0[i][j]; + nn[j][i] = nn[i][j]; + mm[j][i] = mm[i][j]; + nm[j][i] = nm[i][j]; + r0[j][i] = r0[i][j]; + e0nm[j][i] = e0nm[i][j]; + r0n[j][i] = r0n[i][j]; + r0m[j][i] = r0m[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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); + double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); + double p1 = 1-nn[i][j]; + double p2 = 1-mm[i][j]; + + double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); + double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); + + etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * + (rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2)); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * + nn[i][j]*mm[i][j]*(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2)); + + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNMCutCoulCut::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(&e0[i][j],sizeof(double),1,fp); + fwrite(&r0[i][j],sizeof(double),1,fp); + fwrite(&nn[i][j],sizeof(double),1,fp); + fwrite(&mm[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 PairNMCutCoulCut::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(&e0[i][j],sizeof(double),1,fp); + fread(&r0[i][j],sizeof(double),1,fp); + fread(&nn[i][j],sizeof(double),1,fp); + fread(&mm[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(&e0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&mm[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 PairNMCutCoulCut::write_restart_settings(FILE *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 PairNMCutCoulCut::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + 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(&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 PairNMCutCoulCut::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairNMCutCoulCut::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\n",i,j, + e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairNMCutCoulCut::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r,forcecoul,forcenm,phicoul,phinm; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq[itype][jtype]) + forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv); + else forcecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + } else forcenm = 0.0; + fforce = (factor_coul*forcecoul + factor_lj*forcenm) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq[itype][jtype]) { + phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv); + eng += factor_coul*phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + phinm = e0nm[itype][jtype] * + (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) - + offset[itype][jtype]; + eng += factor_lj*phinm; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairNMCutCoulCut::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"e0") == 0) return (void *) e0; + if (strcmp(str,"r0") == 0) return (void *) r0; + if (strcmp(str,"nn") == 0) return (void *) nn; + if (strcmp(str,"mm") == 0) return (void *) mm; + return NULL; +} diff --git a/src/MISC/pair_nm_cut_coul_cut.h b/src/MISC/pair_nm_cut_coul_cut.h new file mode 100644 index 0000000000..dfc2c4d413 --- /dev/null +++ b/src/MISC/pair_nm_cut_coul_cut.h @@ -0,0 +1,78 @@ +/* ---------------------------------------------------------------------- + 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(nm/cut/coul/cut,PairNMCutCoulCut) + + +#else + +#ifndef LMP_PAIR_NM_CUT_COUL_CUT_H +#define LMP_PAIR_NM_CUT_COUL_CUT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairNMCutCoulCut : public Pair { + public: + PairNMCutCoulCut(class LAMMPS *); + virtual ~PairNMCutCoulCut(); + + 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 &); + void *extract(const char *, int &); + + protected: + double cut_lj_global,cut_coul_global; + double **cut_lj,**cut_ljsq; + double **cut_coul,**cut_coulsq; + double **e0,**r0,**nn, **mm; + double **nm,**e0nm,**r0n,**r0m,**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: Pair style nm/cut/coul/cut requires atom attribute q + +The atom style defined does not have this attribute. + +*/ diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp new file mode 100644 index 0000000000..b371e3c07d --- /dev/null +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -0,0 +1,590 @@ +/* ---------------------------------------------------------------------- + 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: Julien Devemy (ICCF) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_nm_cut_coul_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "update.h" +#include "integrate.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 + +/* ---------------------------------------------------------------------- */ + +PairNMCutCoulLong::PairNMCutCoulLong(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + ftable = NULL; + qdist = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +PairNMCutCoulLong::~PairNMCutCoulLong() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(e0); + memory->destroy(r0); + memory->destroy(nn); + memory->destroy(mm); + memory->destroy(nm); + memory->destroy(e0nm); + memory->destroy(r0n); + memory->destroy(r0m); + memory->destroy(offset); + } + if (ftable) free_tables(); +} + +/* ---------------------------------------------------------------------- */ + +void PairNMCutCoulLong::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype,itable; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double fraction,table; + double r,r2inv,factor_coul,factor_lj; + double forcecoul,forcenm,rminv,rninv; + double grij,expm2,prefactor,t,erfc; + int *ilist,*jlist,*numneigh,**firstneigh; + double rsq; + + 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]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + 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; + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + itable = rsq_lookup.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + rminv = pow(r2inv,mm[itype][jtype]/2.0); + rninv = pow(r2inv,nn[itype][jtype]/2.0); + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + } else forcenm = 0.0; + + fpair = (forcecoul + factor_lj*forcenm) * 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) { + if (!ncoultablebits || rsq <= tabinnersq) + ecoul = prefactor*erfc; + else { + table = etable[itable] + fraction*detable[itable]; + ecoul = qtmp*q[j] * table; + } + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = e0nm[itype][jtype] * + (mm[itype][jtype]*r0n[itype][jtype]*rninv - + nn[itype][jtype]*r0m[itype][jtype]*rminv) - 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 PairNMCutCoulLong::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(e0,n+1,n+1,"pair:e0"); + memory->create(r0,n+1,n+1,"pair:r0"); + memory->create(nn,n+1,n+1,"pair:nn"); + memory->create(mm,n+1,n+1,"pair:mm"); + memory->create(nm,n+1,n+1,"pair:nm"); + memory->create(e0nm,n+1,n+1,"pair:e0nm"); + memory->create(r0n,n+1,n+1,"pair:r0n"); + memory->create(r0m,n+1,n+1,"pair:r0m"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); + + cut_lj_global = force->numeric(FLERR,arg[0]); + if (narg == 1) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[1]); + + // 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 PairNMCutCoulLong::coeff(int narg, char **arg) +{ + if (narg < 6 || 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 e0_one = force->numeric(FLERR,arg[2]); + double r0_one = force->numeric(FLERR,arg[3]); + double nn_one = force->numeric(FLERR,arg[4]); + double mm_one = force->numeric(FLERR,arg[5]); + + double cut_lj_one = cut_lj_global; + if (narg == 7) cut_lj_one = force->numeric(FLERR,arg[4]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + e0[i][j] = e0_one; + r0[i][j] = r0_one; + nn[i][j] = nn_one; + mm[i][j] = mm_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 PairNMCutCoulLong::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style nm/cut/coul/long requires atom attribute q"); + + neighbor->request(this); + + cut_coulsq = cut_coul * cut_coul; + // 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; + + // setup force tables + + if (ncoultablebits) init_tables(cut_coul,NULL); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairNMCutCoulLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + // 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]; + + nm[i][j] = nn[i][j]*mm[i][j]; + e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]); + r0n[i][j] = pow(r0[i][j],nn[i][j]); + r0m[i][j] = pow(r0[i][j],mm[i][j]); + + if (offset_flag) { + offset[i][j] = e0nm[i][j] * + ((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) - + (nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j]))); + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + e0[j][i] = e0[i][j]; + nn[j][i] = nn[i][j]; + mm[j][i] = mm[i][j]; + nm[j][i] = nm[i][j]; + r0[j][i] = r0[i][j]; + e0nm[j][i] = e0nm[i][j]; + r0n[j][i] = r0n[i][j]; + r0m[j][i] = r0m[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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); + double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); + double p1 = 1-nn[i][j]; + double p2 = 1-mm[i][j]; + + double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); + double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); + + etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * + (rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2)); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j]*nn[i][j]*mm[i][j] * + (rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2)); + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::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(&e0[i][j],sizeof(double),1,fp); + fwrite(&r0[i][j],sizeof(double),1,fp); + fwrite(&nn[i][j],sizeof(double),1,fp); + fwrite(&mm[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::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(&e0[i][j],sizeof(double),1,fp); + fread(&r0[i][j],sizeof(double),1,fp); + fread(&nn[i][j],sizeof(double),1,fp); + fread(&mm[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&mm[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 PairNMCutCoulLong::write_restart_settings(FILE *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); + fwrite(&ncoultablebits,sizeof(int),1,fp); + fwrite(&tabinner,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + 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); + fread(&ncoultablebits,sizeof(int),1,fp); + fread(&tabinner,sizeof(double),1,fp); + } + 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); + MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world); + MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairNMCutCoulLong::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\n",i,j, + e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairNMCutCoulLong::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r,grij,expm2,t,erfc,prefactor; + double fraction,table,forcecoul,forcenm,phicoul,phinm; + int itable; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + 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; + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + union_int_float_t rsq_lookup_single; + rsq_lookup_single.f = rsq; + itable = rsq_lookup_single.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = atom->q[i]*atom->q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = atom->q[i]*atom->q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + forcenm = e0nm[itype][jtype]*nm[itype][jtype] * + (r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + r0m[itype][jtype]/pow(r,mm[itype][jtype])); + } else forcenm = 0.0; + + fforce = (forcecoul + factor_lj*forcenm) * r2inv; + + double eng = 0.0; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + phicoul = prefactor*erfc; + else { + table = etable[itable] + fraction*detable[itable]; + phicoul = atom->q[i]*atom->q[j] * table; + } + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + + if (rsq < cut_ljsq[itype][jtype]) { + phinm = e0nm[itype][jtype] * + (mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) - + nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) - + offset[itype][jtype]; + eng += factor_lj*phinm; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairNMCutCoulLong::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"e0") == 0) return (void *) e0; + if (strcmp(str,"r0") == 0) return (void *) r0; + if (strcmp(str,"nn") == 0) return (void *) nn; + if (strcmp(str,"mm") == 0) return (void *) mm; + return NULL; +} diff --git a/src/MISC/pair_nm_cut_coul_long.h b/src/MISC/pair_nm_cut_coul_long.h new file mode 100644 index 0000000000..59b1b44672 --- /dev/null +++ b/src/MISC/pair_nm_cut_coul_long.h @@ -0,0 +1,84 @@ +/* ---------------------------------------------------------------------- + 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(nm/cut/coul/long,PairNMCutCoulLong) + +#else + +#ifndef LMP_PAIR_NM_CUT_COUL_LONG_H +#define LMP_PAIR_NM_CUT_COUL_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairNMCutCoulLong : public Pair { + public: + PairNMCutCoulLong(class LAMMPS *); + virtual ~PairNMCutCoulLong(); + + 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 &); + + void *extract(const char *, int &); + + protected: + double cut_lj_global; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **e0,**r0,**nn, **mm; + double **nm,**e0nm,**r0n,**r0m,**offset; + double qdist; // TIP4P distance from O site to negative charge + double g_ewald; + + 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 nm/cut/coul/long requires atom attribute q + +The atom style defined does not have this attribute. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +*/