From 8ffacb55ca09ad9ddba72933560156edf62e18ed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 17 Mar 2022 12:20:17 -0400 Subject: [PATCH] enable and apply clang-format --- src/MOLECULE/bond_harmonic.cpp | 91 ++++++++++++++++------------------ 1 file changed, 44 insertions(+), 47 deletions(-) diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 32988d8d0a..47d7f23e9a 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,15 +13,15 @@ #include "bond_harmonic.h" -#include -#include #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -48,12 +47,12 @@ BondHarmonic::~BondHarmonic() void BondHarmonic::compute(int eflag, int vflag) { - int i1,i2,n,type; - double delx,dely,delz,ebond,fbond; - double rsq,r,dr,rk; + int i1, i2, n, type; + double delx, dely, delz, ebond, fbond; + double rsq, r, dr, rk; ebond = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -71,33 +70,35 @@ void BondHarmonic::compute(int eflag, int vflag) dely = x[i1][1] - x[i2][1]; delz = x[i1][2] - x[i2][2]; - rsq = delx*delx + dely*dely + delz*delz; + rsq = delx * delx + dely * dely + delz * delz; r = sqrt(rsq); dr = r - r0[type]; rk = k[type] * dr; // force & energy - if (r > 0.0) fbond = -2.0*rk/r; - else fbond = 0.0; + if (r > 0.0) + fbond = -2.0 * rk / r; + else + fbond = 0.0; - if (eflag) ebond = rk*dr; + if (eflag) ebond = rk * dr; // apply force to each of 2 atoms if (newton_bond || i1 < nlocal) { - f[i1][0] += delx*fbond; - f[i1][1] += dely*fbond; - f[i1][2] += delz*fbond; + f[i1][0] += delx * fbond; + f[i1][1] += dely * fbond; + f[i1][2] += delz * fbond; } if (newton_bond || i2 < nlocal) { - f[i2][0] -= delx*fbond; - f[i2][1] -= dely*fbond; - f[i2][2] -= delz*fbond; + f[i2][0] -= delx * fbond; + f[i2][1] -= dely * fbond; + f[i2][2] -= delz * fbond; } - if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz); + if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz); } } @@ -106,13 +107,13 @@ void BondHarmonic::compute(int eflag, int vflag) void BondHarmonic::allocate() { allocated = 1; - int n = atom->nbondtypes; + int np1 = atom->nbondtypes + 1; - memory->create(k,n+1,"bond:k"); - memory->create(r0,n+1,"bond:r0"); + memory->create(k, np1, "bond:k"); + memory->create(r0, np1, "bond:r0"); - memory->create(setflag,n+1,"bond:setflag"); - for (int i = 1; i <= n; i++) setflag[i] = 0; + memory->create(setflag, np1, "bond:setflag"); + for (int i = 1; i < np1; i++) setflag[i] = 0; } /* ---------------------------------------------------------------------- @@ -121,14 +122,14 @@ void BondHarmonic::allocate() void BondHarmonic::coeff(int narg, char **arg) { - if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients"); + if (narg != 3) error->all(FLERR, "Incorrect args for bond coefficients"); if (!allocated) allocate(); - int ilo,ihi; - utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); + int ilo, ihi; + utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error); - double k_one = utils::numeric(FLERR,arg[1],false,lmp); - double r0_one = utils::numeric(FLERR,arg[2],false,lmp); + double k_one = utils::numeric(FLERR, arg[1], false, lmp); + double r0_one = utils::numeric(FLERR, arg[2], false, lmp); int count = 0; for (int i = ilo; i <= ihi; i++) { @@ -138,7 +139,7 @@ void BondHarmonic::coeff(int narg, char **arg) count++; } - if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients"); } /* ---------------------------------------------------------------------- @@ -156,8 +157,8 @@ double BondHarmonic::equilibrium_distance(int i) void BondHarmonic::write_restart(FILE *fp) { - fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); - fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&k[1], sizeof(double), atom->nbondtypes, fp); + fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp); } /* ---------------------------------------------------------------------- @@ -169,11 +170,11 @@ void BondHarmonic::read_restart(FILE *fp) allocate(); if (comm->me == 0) { - utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); - utils::sfread(FLERR,&r0[1],sizeof(double),atom->nbondtypes,fp,nullptr,error); + utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); + utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error); } - MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); - MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world); + MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world); for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; } @@ -184,21 +185,19 @@ void BondHarmonic::read_restart(FILE *fp) void BondHarmonic::write_data(FILE *fp) { - for (int i = 1; i <= atom->nbondtypes; i++) - fprintf(fp,"%d %g %g\n",i,k[i],r0[i]); + for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], r0[i]); } /* ---------------------------------------------------------------------- */ -double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, - double &fforce) +double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce) { double r = sqrt(rsq); double dr = r - r0[type]; double rk = k[type] * dr; fforce = 0; - if (r > 0.0) fforce = -2.0*rk/r; - return rk*dr; + if (r > 0.0) fforce = -2.0 * rk / r; + return rk * dr; } /* ---------------------------------------------------------------------- @@ -207,9 +206,7 @@ double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, void *BondHarmonic::extract(const char *str, int &dim) { dim = 1; - if (strcmp(str,"kappa")==0) return (void*) k; - if (strcmp(str,"r0")==0) return (void*) r0; + if (strcmp(str, "kappa") == 0) return (void *) k; + if (strcmp(str, "r0") == 0) return (void *) r0; return nullptr; } - -