From ee98f023b67f366b272fc825d76b1e41fcb9bbd0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 29 Jan 2022 08:02:59 -0500 Subject: [PATCH] enable and apply clang-format --- src/EXTRA-FIX/fix_numdiff.cpp | 116 +++++++++++++++++----------------- 1 file changed, 57 insertions(+), 59 deletions(-) diff --git a/src/EXTRA-FIX/fix_numdiff.cpp b/src/EXTRA-FIX/fix_numdiff.cpp index 757d6adab4..97067d316b 100644 --- a/src/EXTRA-FIX/fix_numdiff.cpp +++ b/src/EXTRA-FIX/fix_numdiff.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,22 +17,23 @@ #include "fix_numdiff.h" -#include -#include "atom.h" -#include "domain.h" -#include "update.h" -#include "modify.h" -#include "compute.h" -#include "respa.h" -#include "force.h" -#include "pair.h" -#include "bond.h" #include "angle.h" +#include "atom.h" +#include "bond.h" +#include "compute.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "pair.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -41,20 +41,18 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), id_pe(nullptr), numdiff_forces(nullptr), - temp_x(nullptr), temp_f(nullptr) + Fix(lmp, narg, arg), id_pe(nullptr), numdiff_forces(nullptr), temp_x(nullptr), temp_f(nullptr) { - if (narg < 5) error->all(FLERR,"Illegal fix numdiff command"); + if (narg < 5) error->all(FLERR, "Illegal fix numdiff command"); peratom_flag = 1; peratom_freq = nevery; size_peratom_cols = 3; respa_level_support = 1; - nevery = utils::inumeric(FLERR,arg[3],false,lmp); - delta = utils::numeric(FLERR,arg[4],false,lmp); - if (nevery <= 0 || delta <= 0.0) - error->all(FLERR,"Illegal fix numdiff command"); + nevery = utils::inumeric(FLERR, arg[3], false, lmp); + delta = utils::numeric(FLERR, arg[4], false, lmp); + if (nevery <= 0 || delta <= 0.0) error->all(FLERR, "Illegal fix numdiff command"); std::string cmd = id + std::string("_pe"); id_pe = utils::strdup(cmd); @@ -65,7 +63,7 @@ FixNumDiff::FixNumDiff(LAMMPS *lmp, int narg, char **arg) : maxatom = 0; if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Fix numdiff requires an atom map, see atom_modify"); + error->all(FLERR, "Fix numdiff requires an atom map, see atom_modify"); // perform initial allocation of atom-based arrays // zero numdiff_forces since dump may access it on timestep 0 @@ -84,7 +82,7 @@ FixNumDiff::~FixNumDiff() memory->destroy(temp_f); modify->delete_compute(id_pe); - delete [] id_pe; + delete[] id_pe; } /* ---------------------------------------------------------------------- */ @@ -107,22 +105,26 @@ void FixNumDiff::init() // require consecutive atom IDs if (!atom->tag_enable || !atom->tag_consecutive()) - error->all(FLERR,"Fix numdiff requires consecutive atom IDs"); + error->all(FLERR, "Fix numdiff requires consecutive atom IDs"); // check for PE compute int icompute = modify->find_compute(id_pe); - if (icompute < 0) error->all(FLERR,"Compute ID for fix numdiff does not exist"); + if (icompute < 0) error->all(FLERR, "Compute ID for fix numdiff does not exist"); pe = modify->compute[icompute]; - if (force->pair && force->pair->compute_flag) pair_compute_flag = 1; - else pair_compute_flag = 0; - if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1; - else kspace_compute_flag = 0; + if (force->pair && force->pair->compute_flag) + pair_compute_flag = 1; + else + pair_compute_flag = 0; + if (force->kspace && force->kspace->compute_flag) + kspace_compute_flag = 1; + else + kspace_compute_flag = 0; - if (utils::strmatch(update->integrate_style,"^respa")) { - ilevel_respa = ((Respa *) update->integrate)->nlevels-1; - if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + if (utils::strmatch(update->integrate_style, "^respa")) { + ilevel_respa = ((Respa *) update->integrate)->nlevels - 1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa); } } @@ -130,11 +132,11 @@ void FixNumDiff::init() void FixNumDiff::setup(int vflag) { - if (utils::strmatch(update->integrate_style,"^verlet")) + if (utils::strmatch(update->integrate_style, "^verlet")) post_force(vflag); else { ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); - post_force_respa(vflag,ilevel_respa,0); + post_force_respa(vflag, ilevel_respa, 0); ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); } } @@ -175,7 +177,7 @@ void FixNumDiff::min_post_force(int vflag) void FixNumDiff::calculate_forces() { - int i,j,ilocal; + int i, j, ilocal; double energy; // grow arrays if necessary @@ -202,48 +204,44 @@ void FixNumDiff::calculate_forces() // loop over all atoms in system // compute a finite difference force in each dimension - int flag,allflag; + int flag, allflag; double denominator = 0.5 / delta; int *mask = atom->mask; - int ntotal = static_cast (atom->natoms); + int ntotal = static_cast(atom->natoms); int dimension = domain->dimension; for (tagint m = 1; m <= ntotal; m++) { ilocal = atom->map(m); flag = 0; if ((ilocal >= 0 && ilocal < nlocal) && (mask[ilocal] & groupbit)) flag = 1; - MPI_Allreduce(&flag,&allflag,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&flag, &allflag, 1, MPI_INT, MPI_SUM, world); if (!allflag) continue; for (int idim = 0; idim < dimension; idim++) { - displace_atoms(ilocal,idim,1); + displace_atoms(ilocal, idim, 1); energy = update_energy(); - if (ilocal >= 0 && ilocal < nlocal) - numdiff_forces[ilocal][idim] -= energy; + if (ilocal >= 0 && ilocal < nlocal) numdiff_forces[ilocal][idim] -= energy; - displace_atoms(ilocal,idim,-2); + displace_atoms(ilocal, idim, -2); energy = update_energy(); if (ilocal >= 0 && ilocal < nlocal) { numdiff_forces[ilocal][idim] += energy; numdiff_forces[ilocal][idim] *= denominator; } - restore_atoms(ilocal,idim); + restore_atoms(ilocal, idim); } } - // recompute energy so all contributions are as before + // recompute energy so all contributions are as before energy = update_energy(); // restore original forces for owned and ghost atoms for (i = 0; i < nall; i++) - for (j = 0; j < 3; j++) { - f[i][j] = temp_f[i][j]; - } - + for (j = 0; j < 3; j++) { f[i][j] = temp_f[i][j]; } } /* ---------------------------------------------------------------------- @@ -257,11 +255,11 @@ void FixNumDiff::displace_atoms(int ilocal, int idim, int magnitude) double **x = atom->x; int *sametag = atom->sametag; int j = ilocal; - x[ilocal][idim] += delta*magnitude; + x[ilocal][idim] += delta * magnitude; while (sametag[j] >= 0) { j = sametag[j]; - x[j][idim] += delta*magnitude; + x[j][idim] += delta * magnitude; } } @@ -295,16 +293,16 @@ double FixNumDiff::update_energy() int eflag = 1; - if (pair_compute_flag) force->pair->compute(eflag,0); + if (pair_compute_flag) force->pair->compute(eflag, 0); if (atom->molecular != Atom::ATOMIC) { - if (force->bond) force->bond->compute(eflag,0); - if (force->angle) force->angle->compute(eflag,0); - if (force->dihedral) force->dihedral->compute(eflag,0); - if (force->improper) force->improper->compute(eflag,0); + if (force->bond) force->bond->compute(eflag, 0); + if (force->angle) force->angle->compute(eflag, 0); + if (force->dihedral) force->dihedral->compute(eflag, 0); + if (force->improper) force->improper->compute(eflag, 0); } - if (kspace_compute_flag) force->kspace->compute(eflag,0); + if (kspace_compute_flag) force->kspace->compute(eflag, 0); double energy = pe->compute_scalar(); return energy; @@ -318,7 +316,7 @@ void FixNumDiff::force_clear(double **forces) { size_t nbytes = sizeof(double) * atom->nlocal; if (force->newton) nbytes += sizeof(double) * atom->nghost; - if (nbytes) memset(&forces[0][0],0,3*nbytes); + if (nbytes) memset(&forces[0][0], 0, 3 * nbytes); } /* ---------------------------------------------------------------------- @@ -331,9 +329,9 @@ void FixNumDiff::reallocate() memory->destroy(temp_x); memory->destroy(temp_f); maxatom = atom->nmax; - memory->create(numdiff_forces,maxatom,3,"numdiff:numdiff_force"); - memory->create(temp_x,maxatom,3,"numdiff:temp_x"); - memory->create(temp_f,maxatom,3,"numdiff:temp_f"); + memory->create(numdiff_forces, maxatom, 3, "numdiff:numdiff_force"); + memory->create(temp_x, maxatom, 3, "numdiff:temp_x"); + memory->create(temp_f, maxatom, 3, "numdiff:temp_f"); array_atom = numdiff_forces; } @@ -344,6 +342,6 @@ void FixNumDiff::reallocate() double FixNumDiff::memory_usage() { double bytes = 0.0; - bytes += (double)3 * maxatom*3 * sizeof(double); + bytes += (double) 3 * maxatom * 3 * sizeof(double); return bytes; }