From 6ce9e2283ee659b5f34c03aa4bbca6210ddc5110 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 7 Apr 2023 18:19:06 -0400 Subject: [PATCH] enable and apply clang-format --- src/pair_lj_expand.cpp | 253 ++++++++++++++++++++--------------------- 1 file changed, 124 insertions(+), 129 deletions(-) diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index ea2801abb3..05b763429b 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,16 +13,16 @@ #include "pair_lj_expand.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -61,14 +60,14 @@ PairLJExpand::~PairLJExpand() void PairLJExpand::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,r6inv,forcelj,factor_lj; - double r,rshift,rshiftsq; - 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, r6inv, forcelj, factor_lj; + double r, rshift, rshiftsq; + int *ilist, *jlist, *numneigh, **firstneigh; evdwl = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -101,35 +100,33 @@ void PairLJExpand::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]) { r = sqrt(rsq); rshift = r - shift[itype][jtype]; - rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - fpair = factor_lj*forcelj/rshift/r; + rshiftsq = rshift * rshift; + r2inv = 1.0 / rshiftsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); + fpair = factor_lj * forcelj / rshift / r; - 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) { - evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - - offset[itype][jtype]; + evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; evdwl *= factor_lj; } - 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); } } } @@ -144,24 +141,23 @@ void PairLJExpand::compute(int eflag, int vflag) void PairLJExpand::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(cutsq, np1, np1, "pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(shift,n+1,n+1,"pair:shift"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); - memory->create(offset,n+1,n+1,"pair:offset"); + memory->create(cut, np1, np1, "pair:cut"); + memory->create(epsilon, np1, np1, "pair:epsilon"); + memory->create(sigma, np1, np1, "pair:sigma"); + memory->create(shift, np1, np1, "pair:shift"); + memory->create(lj1, np1, np1, "pair:lj1"); + memory->create(lj2, np1, np1, "pair:lj2"); + memory->create(lj3, np1, np1, "pair:lj3"); + memory->create(lj4, np1, np1, "pair:lj4"); + memory->create(offset, np1, np1, "pair:offset"); } /* ---------------------------------------------------------------------- @@ -170,14 +166,14 @@ void PairLJExpand::allocate() void PairLJExpand::settings(int narg, char **arg) { - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); - cut_global = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR, arg[0], 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; @@ -190,23 +186,23 @@ void PairLJExpand::settings(int narg, char **arg) void PairLJExpand::coeff(int narg, char **arg) { - if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5 || narg > 6) 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 epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); - double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); - double shift_one = utils::numeric(FLERR,arg[4],false,lmp); + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_one = utils::numeric(FLERR, arg[3], false, lmp); + double shift_one = utils::numeric(FLERR, arg[4], false, lmp); double cut_one = cut_global; - if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp); + if (narg == 6) cut_one = utils::numeric(FLERR, arg[5], 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++) { epsilon[i][j] = epsilon_one; sigma[i][j] = sigma_one; shift[i][j] = shift_one; @@ -216,7 +212,7 @@ void PairLJExpand::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"); } /* ---------------------------------------------------------------------- @@ -228,22 +224,22 @@ double PairLJExpand::init_one(int i, int j) // always mix shift arithmetically if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]); + cut[i][j] = mix_distance(cut[i][i], cut[j][j]); shift[i][j] = 0.5 * (shift[i][i] + shift[j][j]); } - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); if (offset_flag && (cut[i][j] > 0.0)) { - double ratio = sigma[i][j] / cut[i][j]; - offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); - } else offset[i][j] = 0.0; + double ratio = sigma[i][j] / (cut[i][j] + shift[i][j]); + offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0)); + } else + offset[i][j] = 0.0; lj1[j][i] = lj1[i][j]; lj2[j][i] = lj2[i][j]; @@ -259,32 +255,34 @@ double PairLJExpand::init_one(int i, int j) int *type = atom->type; int nlocal = atom->nlocal; - double count[2],all[2]; + 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); + MPI_Allreduce(count, all, 2, MPI_DOUBLE, MPI_SUM, world); - double sig2 = sigma[i][j]*sigma[i][j]; - double sig6 = sig2*sig2*sig2; + double sig2 = sigma[i][j] * sigma[i][j]; + double sig6 = sig2 * sig2 * sig2; double rc1 = cut[i][j]; - double rc2 = rc1*rc1; - double rc3 = rc2*rc1; - double rc9 = rc3*rc3*rc3; + double rc2 = rc1 * rc1; + double rc3 = rc2 * rc1; + double rc9 = rc3 * rc3 * rc3; double shift1 = shift[i][j]; - double shift2 = shift1*shift1; - double shift3 = shift2*shift1; + double shift2 = shift1 * shift1; + double shift3 = shift2 * shift1; - etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 * - ((1.0/9.0 + 2.0*shift1/(10.0*rc1) + shift2/(11.0*rc2))*sig6/rc9 - - (1.0/3.0 + 2.0*shift1/(4.0*rc1) + shift2/(5.0*rc2))/rc3); - ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 * - ((1.0/9.0 + 3.0*shift1/(10.0*rc1) + - 3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 - - (1.0/3.0 + 3.0*shift1/(4.0*rc1) + - 3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3); + etail_ij = 8.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 * + ((1.0 / 9.0 + 2.0 * shift1 / (10.0 * rc1) + shift2 / (11.0 * rc2)) * sig6 / rc9 - + (1.0 / 3.0 + 2.0 * shift1 / (4.0 * rc1) + shift2 / (5.0 * rc2)) / rc3); + ptail_ij = 16.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 * + ((1.0 / 9.0 + 3.0 * shift1 / (10.0 * rc1) + 3.0 * shift2 / (11.0 * rc2) + + shift3 / (12.0 * rc3)) * + 2.0 * sig6 / rc9 - + (1.0 / 3.0 + 3.0 * shift1 / (4.0 * rc1) + 3.0 * shift2 / (5.0 * rc2) + + shift3 / (6.0 * rc3)) / + rc3); } return cut[i][j] + shift[i][j]; @@ -298,15 +296,15 @@ void PairLJExpand::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(&epsilon[i][j],sizeof(double),1,fp); - fwrite(&sigma[i][j],sizeof(double),1,fp); - fwrite(&shift[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&shift[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -321,23 +319,23 @@ void PairLJExpand::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,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &shift[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&shift[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&shift[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -348,10 +346,10 @@ void PairLJExpand::read_restart(FILE *fp) void PairLJExpand::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); + 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); } /* ---------------------------------------------------------------------- @@ -361,15 +359,15 @@ void PairLJExpand::write_restart_settings(FILE *fp) void PairLJExpand::read_restart_settings(FILE *fp) { if (comm->me == 0) { - 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,&tail_flag,sizeof(int),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, &tail_flag, sizeof(int), 1, fp, nullptr, error); } - 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); + 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); } /* ---------------------------------------------------------------------- @@ -379,7 +377,7 @@ void PairLJExpand::read_restart_settings(FILE *fp) void PairLJExpand::write_data(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],shift[i][i]); + fprintf(fp, "%d %g %g %g\n", i, epsilon[i][i], sigma[i][i], shift[i][i]); } /* ---------------------------------------------------------------------- @@ -390,29 +388,26 @@ void PairLJExpand::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\n",i,j, - epsilon[i][j],sigma[i][j],shift[i][j],cut[i][j]); + fprintf(fp, "%d %d %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], shift[i][j], cut[i][j]); } /* ---------------------------------------------------------------------- */ double PairLJExpand::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 r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj; + double r, rshift, rshiftsq, r2inv, r6inv, forcelj, philj; r = sqrt(rsq); rshift = r - shift[itype][jtype]; - rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - fforce = factor_lj*forcelj/rshift/r; + rshiftsq = rshift * rshift; + r2inv = 1.0 / rshiftsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); + fforce = factor_lj * forcelj / rshift / r; - philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - - offset[itype][jtype]; - return factor_lj*philj; + philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + return factor_lj * philj; } /* ---------------------------------------------------------------------- */ @@ -420,8 +415,8 @@ double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double r void *PairLJExpand::extract(const char *str, int &dim) { dim = 2; - if (strcmp(str,"epsilon") == 0) return (void *) epsilon; - if (strcmp(str,"sigma") == 0) return (void *) sigma; - if (strcmp(str,"delta") == 0) return (void *) shift; + if (strcmp(str, "epsilon") == 0) return (void *) epsilon; + if (strcmp(str, "sigma") == 0) return (void *) sigma; + if (strcmp(str, "delta") == 0) return (void *) shift; return nullptr; }