diff --git a/src/comm.cpp b/src/comm.cpp index ad0c836432..7930b08f87 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -243,6 +243,8 @@ void Comm::init() if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1; // Can't used multi2 communication with Newton off + // TODO: need to somehow restrict this option with full neighbor lists + // CANNOT use multi2 communication with full nlist if (force->newton == 0 && multi2) error->all(FLERR,"Cannot use multi2 communication with Newton off"); } diff --git a/src/pair_full_print.cpp b/src/pair_full_print.cpp new file mode 100644 index 0000000000..bf42a81288 --- /dev/null +++ b/src/pair_full_print.cpp @@ -0,0 +1,341 @@ +/* ---------------------------------------------------------------------- + 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 "pair_full_print.h" + +#include +#include +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::PairFullPrint(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairFullPrint::~PairFullPrint() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(prefactor); + memory->destroy(cut); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairFullPrint::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double r,rsq,arg,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + 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]) { + printf("NLIST %d %d %d %d\n", tag[i], tag[j], type[i], type[j]); + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + if (r > 0.0) fpair = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + else fpair = 0.0; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) + evdwl = factor_lj * prefactor[itype][jtype] * (1.0+cos(arg)); + + 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 PairFullPrint::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(prefactor,n+1,n+1,"pair:prefactor"); + memory->create(cut,n+1,n+1,"pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairFullPrint::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairFullPrint::coeff(int narg, char **arg) +{ + if (narg < 3 || narg > 4) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); + utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + + double prefactor_one = utils::numeric(FLERR,arg[2],false,lmp); + + double cut_one = cut_global; + if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + prefactor[i][j] = prefactor_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairFullPrint::init_style() { + // need a full neighbor list + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairFullPrint::init_one(int i, int j) +{ + // always mix prefactors geometrically + + if (setflag[i][j] == 0) { + prefactor[i][j] = sqrt(prefactor[i][i]*prefactor[j][j]); + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + prefactor[j][i] = prefactor[i][j]; + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::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(&prefactor[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairFullPrint::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + utils::sfread(FLERR,&prefactor[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + } + MPI_Bcast(&prefactor[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairFullPrint::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 PairFullPrint::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g\n",i,prefactor[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairFullPrint::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\n",i,j,prefactor[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairFullPrint::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double r,arg,philj; + + r = sqrt(rsq); + arg = MY_PI*r/cut[itype][jtype]; + fforce = factor_lj * prefactor[itype][jtype] * + sin(arg) * MY_PI/cut[itype][jtype]/r; + + philj = prefactor[itype][jtype] * (1.0+cos(arg)); + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairFullPrint::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"a") == 0) return (void *) prefactor; + return nullptr; +} diff --git a/src/pair_full_print.h b/src/pair_full_print.h new file mode 100644 index 0000000000..31b51f4e97 --- /dev/null +++ b/src/pair_full_print.h @@ -0,0 +1,72 @@ +/* -*- 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(full/print,PairFullPrint) + +#else + +#ifndef LMP_PAIR_FULL_PRINT_H +#define LMP_PAIR_FULL_PRINT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairFullPrint : public Pair { + friend class Pair; + + public: + PairFullPrint(class LAMMPS *); + virtual ~PairFullPrint(); + void init_style(); + 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 **prefactor; + double **cut; + + 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. + +*/