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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-17 12:20:17 -04:00
parent 982a5719c4
commit 8ffacb55ca
1 changed files with 44 additions and 47 deletions
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91
src/MOLECULE/bond_harmonic.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -14,15 +13,15 @@
#include "bond_harmonic.h" #include "bond_harmonic.h"
#include <cmath>
#include <cstring>
#include "atom.h" #include "atom.h"
#include "neighbor.h"
#include "comm.h" #include "comm.h"
#include "error.h"
#include "force.h" #include "force.h"
#include "memory.h" #include "memory.h"
#include "error.h" #include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -48,12 +47,12 @@ BondHarmonic::~BondHarmonic()
void BondHarmonic::compute(int eflag, int vflag) void BondHarmonic::compute(int eflag, int vflag)
{ {
int i1,i2,n,type; int i1, i2, n, type;
double delx,dely,delz,ebond,fbond; double delx, dely, delz, ebond, fbond;
double rsq,r,dr,rk; double rsq, r, dr, rk;
ebond = 0.0; ebond = 0.0;
ev_init(eflag,vflag); ev_init(eflag, vflag);
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
@ -71,33 +70,35 @@ void BondHarmonic::compute(int eflag, int vflag)
dely = x[i1][1] - x[i2][1]; dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2]; delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz; rsq = delx * delx + dely * dely + delz * delz;
r = sqrt(rsq); r = sqrt(rsq);
dr = r - r0[type]; dr = r - r0[type];
rk = k[type] * dr; rk = k[type] * dr;
// force & energy // force & energy
if (r > 0.0) fbond = -2.0*rk/r; if (r > 0.0)
else fbond = 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 // apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) { if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond; f[i1][0] += delx * fbond;
f[i1][1] += dely*fbond; f[i1][1] += dely * fbond;
f[i1][2] += delz*fbond; f[i1][2] += delz * fbond;
} }
if (newton_bond || i2 < nlocal) { if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond; f[i2][0] -= delx * fbond;
f[i2][1] -= dely*fbond; f[i2][1] -= dely * fbond;
f[i2][2] -= delz*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() void BondHarmonic::allocate()
{ {
allocated = 1; allocated = 1;
int n = atom->nbondtypes; int np1 = atom->nbondtypes + 1;
memory->create(k,n+1,"bond:k"); memory->create(k, np1, "bond:k");
memory->create(r0,n+1,"bond:r0"); memory->create(r0, np1, "bond:r0");
memory->create(setflag,n+1,"bond:setflag"); memory->create(setflag, np1, "bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0; for (int i = 1; i < np1; i++) setflag[i] = 0;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -121,14 +122,14 @@ void BondHarmonic::allocate()
void BondHarmonic::coeff(int narg, char **arg) 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(); if (!allocated) allocate();
int ilo,ihi; int ilo, ihi;
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error); utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
double k_one = utils::numeric(FLERR,arg[1],false,lmp); double k_one = utils::numeric(FLERR, arg[1], false, lmp);
double r0_one = utils::numeric(FLERR,arg[2],false,lmp); double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
int count = 0; int count = 0;
for (int i = ilo; i <= ihi; i++) { for (int i = ilo; i <= ihi; i++) {
@ -138,7 +139,7 @@ void BondHarmonic::coeff(int narg, char **arg)
count++; 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) void BondHarmonic::write_restart(FILE *fp)
{ {
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
fwrite(&r0[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(); allocate();
if (comm->me == 0) { if (comm->me == 0) {
utils::sfread(FLERR,&k[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); utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
} }
MPI_Bcast(&k[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); MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; 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) void BondHarmonic::write_data(FILE *fp)
{ {
for (int i = 1; i <= atom->nbondtypes; i++) for (int i = 1; i <= atom->nbondtypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], r0[i]);
fprintf(fp,"%d %g %g\n",i,k[i],r0[i]);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
double &fforce)
{ {
double r = sqrt(rsq); double r = sqrt(rsq);
double dr = r - r0[type]; double dr = r - r0[type];
double rk = k[type] * dr; double rk = k[type] * dr;
fforce = 0; fforce = 0;
if (r > 0.0) fforce = -2.0*rk/r; if (r > 0.0) fforce = -2.0 * rk / r;
return rk*dr; 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) void *BondHarmonic::extract(const char *str, int &dim)
{ {
dim = 1; dim = 1;
if (strcmp(str,"kappa")==0) return (void*) k; if (strcmp(str, "kappa") == 0) return (void *) k;
if (strcmp(str,"r0")==0) return (void*) r0; if (strcmp(str, "r0") == 0) return (void *) r0;
return nullptr; return nullptr;
} }