diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index 620ca294c3..e1190b614f 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,14 +13,14 @@ #include "pair_yukawa.h" -#include #include "atom.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include using namespace LAMMPS_NS; @@ -53,13 +52,13 @@ PairYukawa::~PairYukawa() void PairYukawa::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,r,rinv,screening,forceyukawa,factor; - int *ilist,*jlist,*numneigh,**firstneigh; + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; + double rsq, r2inv, r, rinv, screening, forceyukawa, factor; + int *ilist, *jlist, *numneigh, **firstneigh; evdwl = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -92,25 +91,25 @@ void PairYukawa::compute(int eflag, int vflag) delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx * delx + dely * dely + delz * delz; jtype = type[j]; if (rsq < cutsq[itype][jtype]) { - r2inv = 1.0/rsq; + r2inv = 1.0 / rsq; r = sqrt(rsq); - rinv = 1.0/r; - screening = exp(-kappa*r); + rinv = 1.0 / r; + screening = exp(-kappa * r); forceyukawa = a[itype][jtype] * screening * (kappa + rinv); - fpair = factor*forceyukawa * r2inv; + fpair = factor * forceyukawa * r2inv; - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; + 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; + f[j][0] -= delx * fpair; + f[j][1] -= dely * fpair; + f[j][2] -= delz * fpair; } if (eflag) { @@ -118,8 +117,7 @@ void PairYukawa::compute(int eflag, int vflag) evdwl *= factor; } - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); + if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz); } } } @@ -134,18 +132,17 @@ void PairYukawa::compute(int eflag, int vflag) void PairYukawa::allocate() { allocated = 1; - int n = atom->ntypes; + int np1 = atom->ntypes + 1; - 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(setflag, np1, np1, "pair:setflag"); + for (int i = 1; i < np1; i++) + for (int j = i; j < np1; j++) setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(rad,n+1,"pair:rad"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(a,n+1,n+1,"pair:a"); - memory->create(offset,n+1,n+1,"pair:offset"); + memory->create(cutsq, np1, np1, "pair:cutsq"); + memory->create(rad, np1, "pair:rad"); + memory->create(cut, np1, np1, "pair:cut"); + memory->create(a, np1, np1, "pair:a"); + memory->create(offset, np1, np1, "pair:offset"); } /* ---------------------------------------------------------------------- @@ -154,15 +151,15 @@ void PairYukawa::allocate() void PairYukawa::settings(int narg, char **arg) { - if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + if (narg != 2) error->all(FLERR, "Illegal pair_style command"); - kappa = utils::numeric(FLERR,arg[0],false,lmp); - cut_global = utils::numeric(FLERR,arg[1],false,lmp); + kappa = utils::numeric(FLERR, arg[0], false, lmp); + cut_global = utils::numeric(FLERR, arg[1], false, lmp); // reset cutoffs that have been explicitly set if (allocated) { - int i,j; + 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; @@ -175,22 +172,21 @@ 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; - utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); - utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); + 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 a_one = utils::numeric(FLERR,arg[2],false,lmp); + double a_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); + 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++) { + for (int j = MAX(jlo, i); j <= jhi; j++) { a[i][j] = a_one; cut[i][j] = cut_one; setflag[i][j] = 1; @@ -198,7 +194,7 @@ void PairYukawa::coeff(int narg, char **arg) } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -208,14 +204,15 @@ void PairYukawa::coeff(int narg, char **arg) double PairYukawa::init_one(int i, int j) { if (setflag[i][j] == 0) { - a[i][j] = mix_energy(a[i][i],a[j][j],1.0,1.0); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + a[i][j] = mix_energy(a[i][i], a[j][j], 1.0, 1.0); + cut[i][j] = mix_distance(cut[i][i], cut[j][j]); } if (offset_flag && (cut[i][j] > 0.0)) { double screening = exp(-kappa * cut[i][j]); offset[i][j] = a[i][j] * screening / cut[i][j]; - } else offset[i][j] = 0.0; + } else + offset[i][j] = 0.0; a[j][i] = a[i][j]; offset[j][i] = offset[i][j]; @@ -231,13 +228,13 @@ void PairYukawa::write_restart(FILE *fp) { write_restart_settings(fp); - int i,j; + 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); + fwrite(&setflag[i][j], sizeof(int), 1, fp); if (setflag[i][j]) { - fwrite(&a[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&a[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -252,19 +249,19 @@ void PairYukawa::read_restart(FILE *fp) allocate(); - int i,j; + 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 (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,&a[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &a[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&a[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -275,10 +272,10 @@ void PairYukawa::read_restart(FILE *fp) void PairYukawa::write_restart_settings(FILE *fp) { - fwrite(&kappa,sizeof(double),1,fp); - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&kappa, sizeof(double), 1, fp); + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); } /* ---------------------------------------------------------------------- @@ -288,15 +285,15 @@ void PairYukawa::write_restart_settings(FILE *fp) void PairYukawa::read_restart_settings(FILE *fp) { if (comm->me == 0) { - utils::sfread(FLERR,&kappa,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR, &kappa, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); } - MPI_Bcast(&kappa,1,MPI_DOUBLE,0,world); - 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(&kappa, 1, MPI_DOUBLE, 0, world); + 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); } /* ---------------------------------------------------------------------- @@ -305,8 +302,7 @@ void PairYukawa::read_restart_settings(FILE *fp) void PairYukawa::write_data(FILE *fp) { - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g\n",i,a[i][i]); + for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g\n", i, a[i][i]); } /* ---------------------------------------------------------------------- @@ -316,25 +312,23 @@ void PairYukawa::write_data(FILE *fp) void PairYukawa::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,a[i][j],cut[i][j]); + for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g %g\n", i, j, a[i][j], cut[i][j]); } /* ---------------------------------------------------------------------- */ double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, - double /*factor_coul*/, double factor_lj, - double &fforce) + double /*factor_coul*/, double factor_lj, double &fforce) { - double r2inv,r,rinv,screening,forceyukawa,phi; + double r2inv, r, rinv, screening, forceyukawa, phi; - r2inv = 1.0/rsq; + r2inv = 1.0 / rsq; r = sqrt(rsq); - rinv = 1.0/r; - screening = exp(-kappa*r); + rinv = 1.0 / r; + screening = exp(-kappa * r); forceyukawa = a[itype][jtype] * screening * (kappa + rinv); - fforce = factor_lj*forceyukawa * r2inv; + fforce = factor_lj * forceyukawa * r2inv; phi = a[itype][jtype] * screening * rinv - offset[itype][jtype]; - return factor_lj*phi; + return factor_lj * phi; }