From 32612d3f5b432fe936e5a5284c3d00ec5e5a72fb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 18 Mar 2022 00:06:28 -0400 Subject: [PATCH] enable and apply clang-format --- src/angle.cpp | 215 ++++++++++++++-------------- src/bond.cpp | 154 ++++++++++---------- src/dihedral.cpp | 288 +++++++++++++++++++------------------- src/improper.cpp | 281 ++++++++++++++++++------------------- src/table_file_reader.cpp | 10 +- src/timer.cpp | 83 ++++++----- src/tokenizer.cpp | 247 ++++++++++++++++---------------- 7 files changed, 631 insertions(+), 647 deletions(-) diff --git a/src/angle.cpp b/src/angle.cpp index d822418141..52d92b72b2 100644 --- a/src/angle.cpp +++ b/src/angle.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,20 +13,20 @@ #include "angle.h" #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" #include "math_const.h" -#include "suffix.h" -#include "atom_masks.h" #include "memory.h" -#include "error.h" +#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; /* ---------------------------------------------------------------------- */ -Angle::Angle(LAMMPS *lmp) : Pointers(lmp) +Angle::Angle(LAMMPS *_lmp) : Pointers(_lmp) { energy = 0.0; virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0; @@ -67,10 +66,9 @@ Angle::~Angle() void Angle::init() { - if (!allocated && atom->nangletypes) - error->all(FLERR,"Angle coeffs are not set"); + if (!allocated && atom->nangletypes) error->all(FLERR, "Angle coeffs are not set"); for (int i = 1; i <= atom->nangletypes; i++) - if (setflag[i] == 0) error->all(FLERR,"All angle coeffs are not set"); + if (setflag[i] == 0) error->all(FLERR, "All angle coeffs are not set"); init_style(); } @@ -94,7 +92,7 @@ void Angle::init() void Angle::ev_setup(int eflag, int vflag, int alloc) { - int i,n; + int i, n; evflag = 1; @@ -104,11 +102,9 @@ void Angle::ev_setup(int eflag, int vflag, int alloc) vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR); vflag_atom = vflag & VIRIAL_ATOM; - if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) - vflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) vflag_atom = 1; cvflag_atom = 0; - if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) - cvflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) cvflag_atom = 1; vflag_either = vflag_global || vflag_atom || cvflag_atom; // reallocate per-atom arrays if necessary @@ -117,28 +113,29 @@ void Angle::ev_setup(int eflag, int vflag, int alloc) maxeatom = atom->nmax; if (alloc) { memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom"); + memory->create(eatom, comm->nthreads * maxeatom, "angle:eatom"); } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; if (alloc) { memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom"); + memory->create(vatom, comm->nthreads * maxvatom, 6, "angle:vatom"); } } if (cvflag_atom && atom->nmax > maxcvatom) { maxcvatom = atom->nmax; if (alloc) { memory->destroy(cvatom); - memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom"); + memory->create(cvatom, comm->nthreads * maxcvatom, 9, "angle:cvatom"); } } // zero accumulators if (eflag_global) energy = 0.0; - if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; + if (vflag_global) + for (i = 0; i < 6; i++) virial[i] = 0.0; if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; @@ -179,25 +176,25 @@ void Angle::ev_setup(int eflag, int vflag, int alloc) virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3 ------------------------------------------------------------------------- */ -void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, - double eangle, double *f1, double *f3, - double delx1, double dely1, double delz1, - double delx2, double dely2, double delz2) +void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, double eangle, double *f1, + double *f3, double delx1, double dely1, double delz1, double delx2, + double dely2, double delz2) { - double eanglethird,v[6]; + double eanglethird, v[6]; if (eflag_either) { if (eflag_global) { - if (newton_bond) energy += eangle; + if (newton_bond) + energy += eangle; else { - eanglethird = THIRD*eangle; + eanglethird = THIRD * eangle; if (i < nlocal) energy += eanglethird; if (j < nlocal) energy += eanglethird; if (k < nlocal) energy += eanglethird; } } if (eflag_atom) { - eanglethird = THIRD*eangle; + eanglethird = THIRD * eangle; if (newton_bond || i < nlocal) eatom[i] += eanglethird; if (newton_bond || j < nlocal) eatom[j] += eanglethird; if (newton_bond || k < nlocal) eatom[k] += eanglethird; @@ -205,12 +202,12 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, } if (vflag_either) { - v[0] = delx1*f1[0] + delx2*f3[0]; - v[1] = dely1*f1[1] + dely2*f3[1]; - v[2] = delz1*f1[2] + delz2*f3[2]; - v[3] = delx1*f1[1] + delx2*f3[1]; - v[4] = delx1*f1[2] + delx2*f3[2]; - v[5] = dely1*f1[2] + dely2*f3[2]; + v[0] = delx1 * f1[0] + delx2 * f3[0]; + v[1] = dely1 * f1[1] + dely2 * f3[1]; + v[2] = delz1 * f1[2] + delz2 * f3[2]; + v[3] = delx1 * f1[1] + delx2 * f3[1]; + v[4] = delx1 * f1[2] + delx2 * f3[2]; + v[5] = dely1 * f1[2] + dely2 * f3[2]; if (vflag_global) { if (newton_bond) { @@ -222,56 +219,56 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, virial[5] += v[5]; } else { if (i < nlocal) { - virial[0] += THIRD*v[0]; - virial[1] += THIRD*v[1]; - virial[2] += THIRD*v[2]; - virial[3] += THIRD*v[3]; - virial[4] += THIRD*v[4]; - virial[5] += THIRD*v[5]; + virial[0] += THIRD * v[0]; + virial[1] += THIRD * v[1]; + virial[2] += THIRD * v[2]; + virial[3] += THIRD * v[3]; + virial[4] += THIRD * v[4]; + virial[5] += THIRD * v[5]; } if (j < nlocal) { - virial[0] += THIRD*v[0]; - virial[1] += THIRD*v[1]; - virial[2] += THIRD*v[2]; - virial[3] += THIRD*v[3]; - virial[4] += THIRD*v[4]; - virial[5] += THIRD*v[5]; + virial[0] += THIRD * v[0]; + virial[1] += THIRD * v[1]; + virial[2] += THIRD * v[2]; + virial[3] += THIRD * v[3]; + virial[4] += THIRD * v[4]; + virial[5] += THIRD * v[5]; } if (k < nlocal) { - virial[0] += THIRD*v[0]; - virial[1] += THIRD*v[1]; - virial[2] += THIRD*v[2]; - virial[3] += THIRD*v[3]; - virial[4] += THIRD*v[4]; - virial[5] += THIRD*v[5]; + virial[0] += THIRD * v[0]; + virial[1] += THIRD * v[1]; + virial[2] += THIRD * v[2]; + virial[3] += THIRD * v[3]; + virial[4] += THIRD * v[4]; + virial[5] += THIRD * v[5]; } } } if (vflag_atom) { if (newton_bond || i < nlocal) { - vatom[i][0] += THIRD*v[0]; - vatom[i][1] += THIRD*v[1]; - vatom[i][2] += THIRD*v[2]; - vatom[i][3] += THIRD*v[3]; - vatom[i][4] += THIRD*v[4]; - vatom[i][5] += THIRD*v[5]; + vatom[i][0] += THIRD * v[0]; + vatom[i][1] += THIRD * v[1]; + vatom[i][2] += THIRD * v[2]; + vatom[i][3] += THIRD * v[3]; + vatom[i][4] += THIRD * v[4]; + vatom[i][5] += THIRD * v[5]; } if (newton_bond || j < nlocal) { - vatom[j][0] += THIRD*v[0]; - vatom[j][1] += THIRD*v[1]; - vatom[j][2] += THIRD*v[2]; - vatom[j][3] += THIRD*v[3]; - vatom[j][4] += THIRD*v[4]; - vatom[j][5] += THIRD*v[5]; + vatom[j][0] += THIRD * v[0]; + vatom[j][1] += THIRD * v[1]; + vatom[j][2] += THIRD * v[2]; + vatom[j][3] += THIRD * v[3]; + vatom[j][4] += THIRD * v[4]; + vatom[j][5] += THIRD * v[5]; } if (newton_bond || k < nlocal) { - vatom[k][0] += THIRD*v[0]; - vatom[k][1] += THIRD*v[1]; - vatom[k][2] += THIRD*v[2]; - vatom[k][3] += THIRD*v[3]; - vatom[k][4] += THIRD*v[4]; - vatom[k][5] += THIRD*v[5]; + vatom[k][0] += THIRD * v[0]; + vatom[k][1] += THIRD * v[1]; + vatom[k][2] += THIRD * v[2]; + vatom[k][3] += THIRD * v[3]; + vatom[k][4] += THIRD * v[4]; + vatom[k][5] += THIRD * v[5]; } } } @@ -289,60 +286,60 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, double a1[3]; // a1 = r10 = (2*r12 - r32)/3 - a1[0] = THIRD*(2*delx1-delx2); - a1[1] = THIRD*(2*dely1-dely2); - a1[2] = THIRD*(2*delz1-delz2); + a1[0] = THIRD * (2 * delx1 - delx2); + a1[1] = THIRD * (2 * dely1 - dely2); + a1[2] = THIRD * (2 * delz1 - delz2); - cvatom[i][0] += a1[0]*f1[0]; - cvatom[i][1] += a1[1]*f1[1]; - cvatom[i][2] += a1[2]*f1[2]; - cvatom[i][3] += a1[0]*f1[1]; - cvatom[i][4] += a1[0]*f1[2]; - cvatom[i][5] += a1[1]*f1[2]; - cvatom[i][6] += a1[1]*f1[0]; - cvatom[i][7] += a1[2]*f1[0]; - cvatom[i][8] += a1[2]*f1[1]; + cvatom[i][0] += a1[0] * f1[0]; + cvatom[i][1] += a1[1] * f1[1]; + cvatom[i][2] += a1[2] * f1[2]; + cvatom[i][3] += a1[0] * f1[1]; + cvatom[i][4] += a1[0] * f1[2]; + cvatom[i][5] += a1[1] * f1[2]; + cvatom[i][6] += a1[1] * f1[0]; + cvatom[i][7] += a1[2] * f1[0]; + cvatom[i][8] += a1[2] * f1[1]; } if (newton_bond || j < nlocal) { double a2[3]; double f2[3]; // a2 = r20 = ( -r12 - r32)/3 - a2[0] = THIRD*(-delx1-delx2); - a2[1] = THIRD*(-dely1-dely2); - a2[2] = THIRD*(-delz1-delz2); + a2[0] = THIRD * (-delx1 - delx2); + a2[1] = THIRD * (-dely1 - dely2); + a2[2] = THIRD * (-delz1 - delz2); - f2[0] = - f1[0] - f3[0]; - f2[1] = - f1[1] - f3[1]; - f2[2] = - f1[2] - f3[2]; + f2[0] = -f1[0] - f3[0]; + f2[1] = -f1[1] - f3[1]; + f2[2] = -f1[2] - f3[2]; - cvatom[j][0] += a2[0]*f2[0]; - cvatom[j][1] += a2[1]*f2[1]; - cvatom[j][2] += a2[2]*f2[2]; - cvatom[j][3] += a2[0]*f2[1]; - cvatom[j][4] += a2[0]*f2[2]; - cvatom[j][5] += a2[1]*f2[2]; - cvatom[j][6] += a2[1]*f2[0]; - cvatom[j][7] += a2[2]*f2[0]; - cvatom[j][8] += a2[2]*f2[1]; + cvatom[j][0] += a2[0] * f2[0]; + cvatom[j][1] += a2[1] * f2[1]; + cvatom[j][2] += a2[2] * f2[2]; + cvatom[j][3] += a2[0] * f2[1]; + cvatom[j][4] += a2[0] * f2[2]; + cvatom[j][5] += a2[1] * f2[2]; + cvatom[j][6] += a2[1] * f2[0]; + cvatom[j][7] += a2[2] * f2[0]; + cvatom[j][8] += a2[2] * f2[1]; } if (newton_bond || k < nlocal) { double a3[3]; // a3 = r30 = ( -r12 + 2*r32)/3 - a3[0] = THIRD*(-delx1+2*delx2); - a3[1] = THIRD*(-dely1+2*dely2); - a3[2] = THIRD*(-delz1+2*delz2); + a3[0] = THIRD * (-delx1 + 2 * delx2); + a3[1] = THIRD * (-dely1 + 2 * dely2); + a3[2] = THIRD * (-delz1 + 2 * delz2); - cvatom[k][0] += a3[0]*f3[0]; - cvatom[k][1] += a3[1]*f3[1]; - cvatom[k][2] += a3[2]*f3[2]; - cvatom[k][3] += a3[0]*f3[1]; - cvatom[k][4] += a3[0]*f3[2]; - cvatom[k][5] += a3[1]*f3[2]; - cvatom[k][6] += a3[1]*f3[0]; - cvatom[k][7] += a3[2]*f3[0]; - cvatom[k][8] += a3[2]*f3[1]; + cvatom[k][0] += a3[0] * f3[0]; + cvatom[k][1] += a3[1] * f3[1]; + cvatom[k][2] += a3[2] * f3[2]; + cvatom[k][3] += a3[0] * f3[1]; + cvatom[k][4] += a3[0] * f3[2]; + cvatom[k][5] += a3[1] * f3[2]; + cvatom[k][6] += a3[1] * f3[0]; + cvatom[k][7] += a3[2] * f3[0]; + cvatom[k][8] += a3[2] * f3[1]; } } } @@ -351,8 +348,8 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond, double Angle::memory_usage() { - double bytes = (double)comm->nthreads*maxeatom * sizeof(double); - bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double); - bytes += (double)comm->nthreads*maxcvatom*9 * sizeof(double); + double bytes = (double) comm->nthreads * maxeatom * sizeof(double); + bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double); + bytes += (double) comm->nthreads * maxcvatom * 9 * sizeof(double); return bytes; } diff --git a/src/bond.cpp b/src/bond.cpp index fb313f0170..332e65de9f 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -26,14 +25,14 @@ using namespace LAMMPS_NS; -enum{NONE,LINEAR,SPLINE}; +enum { NONE, LINEAR, SPLINE }; /* ----------------------------------------------------------------------- set bond contribution to Vdwl energy to 0.0 a particular bond style can override this ------------------------------------------------------------------------- */ -Bond::Bond(LAMMPS *lmp) : Pointers(lmp) +Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp) { energy = 0.0; virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0; @@ -70,10 +69,9 @@ Bond::~Bond() void Bond::init() { - if (!allocated && atom->nbondtypes) - error->all(FLERR,"Bond coeffs are not set"); + if (!allocated && atom->nbondtypes) error->all(FLERR, "Bond coeffs are not set"); for (int i = 1; i <= atom->nbondtypes; i++) - if (setflag[i] == 0) error->all(FLERR,"All bond coeffs are not set"); + if (setflag[i] == 0) error->all(FLERR, "All bond coeffs are not set"); init_style(); } @@ -93,7 +91,7 @@ void Bond::init() void Bond::ev_setup(int eflag, int vflag, int alloc) { - int i,n; + int i, n; evflag = 1; @@ -111,21 +109,22 @@ void Bond::ev_setup(int eflag, int vflag, int alloc) maxeatom = atom->nmax; if (alloc) { memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"bond:eatom"); + memory->create(eatom, comm->nthreads * maxeatom, "bond:eatom"); } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; if (alloc) { memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"bond:vatom"); + memory->create(vatom, comm->nthreads * maxvatom, 6, "bond:vatom"); } } // zero accumulators if (eflag_global) energy = 0.0; - if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; + if (vflag_global) + for (i = 0; i < 6; i++) virial[i] = 0.0; if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; @@ -149,35 +148,35 @@ void Bond::ev_setup(int eflag, int vflag, int alloc) tally energy and virial into global and per-atom accumulators ------------------------------------------------------------------------- */ -void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, - double ebond, double fbond, +void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, double ebond, double fbond, double delx, double dely, double delz) { - double ebondhalf,v[6]; + double ebondhalf, v[6]; if (eflag_either) { if (eflag_global) { - if (newton_bond) energy += ebond; + if (newton_bond) + energy += ebond; else { - ebondhalf = 0.5*ebond; + ebondhalf = 0.5 * ebond; if (i < nlocal) energy += ebondhalf; if (j < nlocal) energy += ebondhalf; } } if (eflag_atom) { - ebondhalf = 0.5*ebond; + ebondhalf = 0.5 * ebond; if (newton_bond || i < nlocal) eatom[i] += ebondhalf; if (newton_bond || j < nlocal) eatom[j] += ebondhalf; } } if (vflag_either) { - v[0] = delx*delx*fbond; - v[1] = dely*dely*fbond; - v[2] = delz*delz*fbond; - v[3] = delx*dely*fbond; - v[4] = delx*delz*fbond; - v[5] = dely*delz*fbond; + v[0] = delx * delx * fbond; + v[1] = dely * dely * fbond; + v[2] = delz * delz * fbond; + v[3] = delx * dely * fbond; + v[4] = delx * delz * fbond; + v[5] = dely * delz * fbond; if (vflag_global) { if (newton_bond) { @@ -189,40 +188,40 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, virial[5] += v[5]; } else { if (i < nlocal) { - virial[0] += 0.5*v[0]; - virial[1] += 0.5*v[1]; - virial[2] += 0.5*v[2]; - virial[3] += 0.5*v[3]; - virial[4] += 0.5*v[4]; - virial[5] += 0.5*v[5]; + virial[0] += 0.5 * v[0]; + virial[1] += 0.5 * v[1]; + virial[2] += 0.5 * v[2]; + virial[3] += 0.5 * v[3]; + virial[4] += 0.5 * v[4]; + virial[5] += 0.5 * v[5]; } if (j < nlocal) { - virial[0] += 0.5*v[0]; - virial[1] += 0.5*v[1]; - virial[2] += 0.5*v[2]; - virial[3] += 0.5*v[3]; - virial[4] += 0.5*v[4]; - virial[5] += 0.5*v[5]; + virial[0] += 0.5 * v[0]; + virial[1] += 0.5 * v[1]; + virial[2] += 0.5 * v[2]; + virial[3] += 0.5 * v[3]; + virial[4] += 0.5 * v[4]; + virial[5] += 0.5 * v[5]; } } } if (vflag_atom) { if (newton_bond || i < nlocal) { - vatom[i][0] += 0.5*v[0]; - vatom[i][1] += 0.5*v[1]; - vatom[i][2] += 0.5*v[2]; - vatom[i][3] += 0.5*v[3]; - vatom[i][4] += 0.5*v[4]; - vatom[i][5] += 0.5*v[5]; + vatom[i][0] += 0.5 * v[0]; + vatom[i][1] += 0.5 * v[1]; + vatom[i][2] += 0.5 * v[2]; + vatom[i][3] += 0.5 * v[3]; + vatom[i][4] += 0.5 * v[4]; + vatom[i][5] += 0.5 * v[5]; } if (newton_bond || j < nlocal) { - vatom[j][0] += 0.5*v[0]; - vatom[j][1] += 0.5*v[1]; - vatom[j][2] += 0.5*v[2]; - vatom[j][3] += 0.5*v[3]; - vatom[j][4] += 0.5*v[4]; - vatom[j][5] += 0.5*v[5]; + vatom[j][0] += 0.5 * v[0]; + vatom[j][1] += 0.5 * v[1]; + vatom[j][2] += 0.5 * v[2]; + vatom[j][3] += 0.5 * v[3]; + vatom[j][4] += 0.5 * v[4]; + vatom[j][5] += 0.5 * v[5]; } } } @@ -234,26 +233,25 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, void Bond::write_file(int narg, char **arg) { - if (narg != 6 && narg !=8) error->all(FLERR,"Illegal bond_write command"); + if (narg != 6 && narg != 8) error->all(FLERR, "Illegal bond_write command"); // parse optional arguments int itype = 0; int jtype = 0; if (narg == 8) { - itype = utils::inumeric(FLERR,arg[6],false,lmp); - jtype = utils::inumeric(FLERR,arg[7],false,lmp); + itype = utils::inumeric(FLERR, arg[6], false, lmp); + jtype = utils::inumeric(FLERR, arg[7], false, lmp); if (itype < 1 || itype > atom->ntypes || jtype < 1 || jtype > atom->ntypes) - error->all(FLERR,"Invalid atom types in bond_write command"); + error->all(FLERR, "Invalid atom types in bond_write command"); } - int btype = utils::inumeric(FLERR,arg[0],false,lmp); - int n = utils::inumeric(FLERR,arg[1],false,lmp); - double inner = utils::numeric(FLERR,arg[2],false,lmp); - double outer = utils::numeric(FLERR,arg[3],false,lmp); + int btype = utils::inumeric(FLERR, arg[0], false, lmp); + int n = utils::inumeric(FLERR, arg[1], false, lmp); + double inner = utils::numeric(FLERR, arg[2], false, lmp); + double outer = utils::numeric(FLERR, arg[3], false, lmp); if (inner <= 0.0 || inner >= outer) - error->all(FLERR,"Invalid rlo/rhi values in bond_write command"); - + error->all(FLERR, "Invalid rlo/rhi values in bond_write command"); double r0 = equilibrium_distance(btype); @@ -271,23 +269,24 @@ void Bond::write_file(int narg, char **arg) // - if the file already exists, print a message about appending // while printing the date and check that units are consistent. if (platform::file_is_readable(table_file)) { - std::string units = utils::get_potential_units(table_file,"table"); + std::string units = utils::get_potential_units(table_file, "table"); if (!units.empty() && (units != update->unit_style)) { - error->one(FLERR,"Trying to append to a table file with UNITS: {} while units are {}", + error->one(FLERR, "Trying to append to a table file with UNITS: {} while units are {}", units, update->unit_style); } - std::string date = utils::get_potential_date(table_file,"table"); - utils::logmesg(lmp,"Appending to table file {} with DATE: {}\n", table_file, date); - fp = fopen(table_file.c_str(),"a"); + std::string date = utils::get_potential_date(table_file, "table"); + utils::logmesg(lmp, "Appending to table file {} with DATE: {}\n", table_file, date); + fp = fopen(table_file.c_str(), "a"); } else { - utils::logmesg(lmp,"Creating table file {} with DATE: {}\n", - table_file, utils::current_date()); - fp = fopen(table_file.c_str(),"w"); - if (fp) fmt::print(fp,"# DATE: {} UNITS: {} Created by bond_write\n", - utils::current_date(), update->unit_style); + utils::logmesg(lmp, "Creating table file {} with DATE: {}\n", table_file, + utils::current_date()); + fp = fopen(table_file.c_str(), "w"); + if (fp) + fmt::print(fp, "# DATE: {} UNITS: {} Created by bond_write\n", utils::current_date(), + update->unit_style); } if (fp == nullptr) - error->one(FLERR,"Cannot open bond_write file {}: {}", arg[4], utils::getsyserror()); + error->one(FLERR, "Cannot open bond_write file {}: {}", arg[4], utils::getsyserror()); } // initialize potentials before evaluating bond potential @@ -299,20 +298,20 @@ void Bond::write_file(int narg, char **arg) neighbor->init(); if (comm->me == 0) { - double r,e,f; + double r, e, f; // evaluate energy and force at each of N distances // note that Bond::single() takes r**2 and returns f/r. - fprintf(fp,"# Bond potential %s for bond type %d: i,r,energy,force\n", - force->bond_style,btype); - fprintf(fp,"\n%s\nN %d EQ %.15g\n\n",arg[5],n,r0); + fprintf(fp, "# Bond potential %s for bond type %d: i,r,energy,force\n", force->bond_style, + btype); + fprintf(fp, "\n%s\nN %d EQ %.15g\n\n", arg[5], n, r0); - const double dr = (outer-inner) / static_cast(n-1); + const double dr = (outer - inner) / static_cast(n - 1); for (int i = 0; i < n; i++) { r = inner + dr * static_cast(i); - e = single(btype,r*r,itype,jtype,f); - fprintf(fp,"%d %.15g %.15g %.15g\n",i+1,r,e,f*r); + e = single(btype, r * r, itype, jtype, f); + fprintf(fp, "%d %.15g %.15g %.15g\n", i + 1, r, e, f * r); } fclose(fp); } @@ -322,8 +321,8 @@ void Bond::write_file(int narg, char **arg) double Bond::memory_usage() { - double bytes = (double)comm->nthreads*maxeatom * sizeof(double); - bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double); + double bytes = (double) comm->nthreads * maxeatom * sizeof(double); + bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double); return bytes; } @@ -332,8 +331,7 @@ double Bond::memory_usage() -------------------------------------------------------------------------- */ void Bond::reinit() { - if (!reinitflag) - error->all(FLERR,"Fix adapt interface to this bond style not supported"); + if (!reinitflag) error->all(FLERR, "Fix adapt interface to this bond style not supported"); init(); } diff --git a/src/dihedral.cpp b/src/dihedral.cpp index a0b6746a2c..5b4f923273 100644 --- a/src/dihedral.cpp +++ b/src/dihedral.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -14,11 +13,11 @@ #include "dihedral.h" #include "atom.h" -#include "comm.h" -#include "force.h" #include "atom_masks.h" -#include "memory.h" +#include "comm.h" #include "error.h" +#include "force.h" +#include "memory.h" #include "suffix.h" #include "update.h" @@ -29,7 +28,7 @@ using namespace LAMMPS_NS; DihedralCharmm will override this ------------------------------------------------------------------------- */ -Dihedral::Dihedral(LAMMPS *lmp) : Pointers(lmp) +Dihedral::Dihedral(LAMMPS *_lmp) : Pointers(_lmp) { energy = 0.0; writedata = 0; @@ -68,10 +67,9 @@ Dihedral::~Dihedral() void Dihedral::init() { - if (!allocated && atom->ndihedraltypes) - error->all(FLERR,"Dihedral coeffs are not set"); + if (!allocated && atom->ndihedraltypes) error->all(FLERR, "Dihedral coeffs are not set"); for (int i = 1; i <= atom->ndihedraltypes; i++) - if (setflag[i] == 0) error->all(FLERR,"All dihedral coeffs are not set"); + if (setflag[i] == 0) error->all(FLERR, "All dihedral coeffs are not set"); init_style(); } @@ -94,7 +92,7 @@ void Dihedral::init() void Dihedral::ev_setup(int eflag, int vflag, int alloc) { - int i,n; + int i, n; evflag = 1; @@ -104,11 +102,9 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc) vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR); vflag_atom = vflag & VIRIAL_ATOM; - if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) - vflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) vflag_atom = 1; cvflag_atom = 0; - if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) - cvflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) cvflag_atom = 1; vflag_either = vflag_global || vflag_atom || cvflag_atom; // reallocate per-atom arrays if necessary @@ -117,28 +113,29 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc) maxeatom = atom->nmax; if (alloc) { memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"dihedral:eatom"); + memory->create(eatom, comm->nthreads * maxeatom, "dihedral:eatom"); } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; if (alloc) { memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"dihedral:vatom"); + memory->create(vatom, comm->nthreads * maxvatom, 6, "dihedral:vatom"); } } if (cvflag_atom && atom->nmax > maxcvatom) { maxcvatom = atom->nmax; if (alloc) { memory->destroy(cvatom); - memory->create(cvatom,comm->nthreads*maxcvatom,9,"dihedral:cvatom"); + memory->create(cvatom, comm->nthreads * maxcvatom, 9, "dihedral:cvatom"); } } // zero accumulators if (eflag_global) energy = 0.0; - if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; + if (vflag_global) + for (i = 0; i < 6; i++) virial[i] = 0.0; if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; @@ -181,20 +178,19 @@ void Dihedral::ev_setup(int eflag, int vflag, int alloc) = vb1*f1 + vb2*f3 + (vb3+vb2)*f4 ------------------------------------------------------------------------- */ -void Dihedral::ev_tally(int i1, int i2, int i3, int i4, - int nlocal, int newton_bond, - double edihedral, double *f1, double *f3, double *f4, - double vb1x, double vb1y, double vb1z, - double vb2x, double vb2y, double vb2z, +void Dihedral::ev_tally(int i1, int i2, int i3, int i4, int nlocal, int newton_bond, + double edihedral, double *f1, double *f3, double *f4, double vb1x, + double vb1y, double vb1z, double vb2x, double vb2y, double vb2z, double vb3x, double vb3y, double vb3z) { - double edihedralquarter,v[6]; + double edihedralquarter, v[6]; if (eflag_either) { if (eflag_global) { - if (newton_bond) energy += edihedral; + if (newton_bond) + energy += edihedral; else { - edihedralquarter = 0.25*edihedral; + edihedralquarter = 0.25 * edihedral; if (i1 < nlocal) energy += edihedralquarter; if (i2 < nlocal) energy += edihedralquarter; if (i3 < nlocal) energy += edihedralquarter; @@ -202,7 +198,7 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4, } } if (eflag_atom) { - edihedralquarter = 0.25*edihedral; + edihedralquarter = 0.25 * edihedral; if (newton_bond || i1 < nlocal) eatom[i1] += edihedralquarter; if (newton_bond || i2 < nlocal) eatom[i2] += edihedralquarter; if (newton_bond || i3 < nlocal) eatom[i3] += edihedralquarter; @@ -211,12 +207,12 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4, } if (vflag_either) { - v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0]; - v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1]; - v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2]; - v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1]; - v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2]; - v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2]; + v[0] = vb1x * f1[0] + vb2x * f3[0] + (vb3x + vb2x) * f4[0]; + v[1] = vb1y * f1[1] + vb2y * f3[1] + (vb3y + vb2y) * f4[1]; + v[2] = vb1z * f1[2] + vb2z * f3[2] + (vb3z + vb2z) * f4[2]; + v[3] = vb1x * f1[1] + vb2x * f3[1] + (vb3x + vb2x) * f4[1]; + v[4] = vb1x * f1[2] + vb2x * f3[2] + (vb3x + vb2x) * f4[2]; + v[5] = vb1y * f1[2] + vb2y * f3[2] + (vb3y + vb2y) * f4[2]; if (vflag_global) { if (newton_bond) { @@ -228,72 +224,72 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4, virial[5] += v[5]; } else { if (i1 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i2 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i3 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i4 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } } } if (vflag_atom) { if (newton_bond || i1 < nlocal) { - vatom[i1][0] += 0.25*v[0]; - vatom[i1][1] += 0.25*v[1]; - vatom[i1][2] += 0.25*v[2]; - vatom[i1][3] += 0.25*v[3]; - vatom[i1][4] += 0.25*v[4]; - vatom[i1][5] += 0.25*v[5]; + vatom[i1][0] += 0.25 * v[0]; + vatom[i1][1] += 0.25 * v[1]; + vatom[i1][2] += 0.25 * v[2]; + vatom[i1][3] += 0.25 * v[3]; + vatom[i1][4] += 0.25 * v[4]; + vatom[i1][5] += 0.25 * v[5]; } if (newton_bond || i2 < nlocal) { - vatom[i2][0] += 0.25*v[0]; - vatom[i2][1] += 0.25*v[1]; - vatom[i2][2] += 0.25*v[2]; - vatom[i2][3] += 0.25*v[3]; - vatom[i2][4] += 0.25*v[4]; - vatom[i2][5] += 0.25*v[5]; + vatom[i2][0] += 0.25 * v[0]; + vatom[i2][1] += 0.25 * v[1]; + vatom[i2][2] += 0.25 * v[2]; + vatom[i2][3] += 0.25 * v[3]; + vatom[i2][4] += 0.25 * v[4]; + vatom[i2][5] += 0.25 * v[5]; } if (newton_bond || i3 < nlocal) { - vatom[i3][0] += 0.25*v[0]; - vatom[i3][1] += 0.25*v[1]; - vatom[i3][2] += 0.25*v[2]; - vatom[i3][3] += 0.25*v[3]; - vatom[i3][4] += 0.25*v[4]; - vatom[i3][5] += 0.25*v[5]; + vatom[i3][0] += 0.25 * v[0]; + vatom[i3][1] += 0.25 * v[1]; + vatom[i3][2] += 0.25 * v[2]; + vatom[i3][3] += 0.25 * v[3]; + vatom[i3][4] += 0.25 * v[4]; + vatom[i3][5] += 0.25 * v[5]; } if (newton_bond || i4 < nlocal) { - vatom[i4][0] += 0.25*v[0]; - vatom[i4][1] += 0.25*v[1]; - vatom[i4][2] += 0.25*v[2]; - vatom[i4][3] += 0.25*v[3]; - vatom[i4][4] += 0.25*v[4]; - vatom[i4][5] += 0.25*v[5]; + vatom[i4][0] += 0.25 * v[0]; + vatom[i4][1] += 0.25 * v[1]; + vatom[i4][2] += 0.25 * v[2]; + vatom[i4][3] += 0.25 * v[3]; + vatom[i4][4] += 0.25 * v[4]; + vatom[i4][5] += 0.25 * v[5]; } } } @@ -312,99 +308,97 @@ void Dihedral::ev_tally(int i1, int i2, int i3, int i4, double a1[3]; // a1 = r10 = (3*r12 - 2*r32 - r43)/4 - a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x); - a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y); - a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z); + a1[0] = 0.25 * (3 * vb1x - 2 * vb2x - vb3x); + a1[1] = 0.25 * (3 * vb1y - 2 * vb2y - vb3y); + a1[2] = 0.25 * (3 * vb1z - 2 * vb2z - vb3z); - cvatom[i1][0] += a1[0]*f1[0]; - cvatom[i1][1] += a1[1]*f1[1]; - cvatom[i1][2] += a1[2]*f1[2]; - cvatom[i1][3] += a1[0]*f1[1]; - cvatom[i1][4] += a1[0]*f1[2]; - cvatom[i1][5] += a1[1]*f1[2]; - cvatom[i1][6] += a1[1]*f1[0]; - cvatom[i1][7] += a1[2]*f1[0]; - cvatom[i1][8] += a1[2]*f1[1]; + cvatom[i1][0] += a1[0] * f1[0]; + cvatom[i1][1] += a1[1] * f1[1]; + cvatom[i1][2] += a1[2] * f1[2]; + cvatom[i1][3] += a1[0] * f1[1]; + cvatom[i1][4] += a1[0] * f1[2]; + cvatom[i1][5] += a1[1] * f1[2]; + cvatom[i1][6] += a1[1] * f1[0]; + cvatom[i1][7] += a1[2] * f1[0]; + cvatom[i1][8] += a1[2] * f1[1]; } if (newton_bond || i2 < nlocal) { double a2[3]; double f2[3]; // a2 = r20 = ( -r12 - 2*r32 - r43)/4 - a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x); - a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y); - a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z); + a2[0] = 0.25 * (-vb1x - 2 * vb2x - vb3x); + a2[1] = 0.25 * (-vb1y - 2 * vb2y - vb3y); + a2[2] = 0.25 * (-vb1z - 2 * vb2z - vb3z); - f2[0] = - f1[0] - f3[0] - f4[0]; - f2[1] = - f1[1] - f3[1] - f4[1]; - f2[2] = - f1[2] - f3[2] - f4[2]; + f2[0] = -f1[0] - f3[0] - f4[0]; + f2[1] = -f1[1] - f3[1] - f4[1]; + f2[2] = -f1[2] - f3[2] - f4[2]; - cvatom[i2][0] += a2[0]*f2[0]; - cvatom[i2][1] += a2[1]*f2[1]; - cvatom[i2][2] += a2[2]*f2[2]; - cvatom[i2][3] += a2[0]*f2[1]; - cvatom[i2][4] += a2[0]*f2[2]; - cvatom[i2][5] += a2[1]*f2[2]; - cvatom[i2][6] += a2[1]*f2[0]; - cvatom[i2][7] += a2[2]*f2[0]; - cvatom[i2][8] += a2[2]*f2[1]; + cvatom[i2][0] += a2[0] * f2[0]; + cvatom[i2][1] += a2[1] * f2[1]; + cvatom[i2][2] += a2[2] * f2[2]; + cvatom[i2][3] += a2[0] * f2[1]; + cvatom[i2][4] += a2[0] * f2[2]; + cvatom[i2][5] += a2[1] * f2[2]; + cvatom[i2][6] += a2[1] * f2[0]; + cvatom[i2][7] += a2[2] * f2[0]; + cvatom[i2][8] += a2[2] * f2[1]; } if (newton_bond || i3 < nlocal) { double a3[3]; // a3 = r30 = ( -r12 + 2*r32 - r43)/4 - a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x); - a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y); - a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z); + a3[0] = 0.25 * (-vb1x + 2 * vb2x - vb3x); + a3[1] = 0.25 * (-vb1y + 2 * vb2y - vb3y); + a3[2] = 0.25 * (-vb1z + 2 * vb2z - vb3z); - cvatom[i3][0] += a3[0]*f3[0]; - cvatom[i3][1] += a3[1]*f3[1]; - cvatom[i3][2] += a3[2]*f3[2]; - cvatom[i3][3] += a3[0]*f3[1]; - cvatom[i3][4] += a3[0]*f3[2]; - cvatom[i3][5] += a3[1]*f3[2]; - cvatom[i3][6] += a3[1]*f3[0]; - cvatom[i3][7] += a3[2]*f3[0]; - cvatom[i3][8] += a3[2]*f3[1]; + cvatom[i3][0] += a3[0] * f3[0]; + cvatom[i3][1] += a3[1] * f3[1]; + cvatom[i3][2] += a3[2] * f3[2]; + cvatom[i3][3] += a3[0] * f3[1]; + cvatom[i3][4] += a3[0] * f3[2]; + cvatom[i3][5] += a3[1] * f3[2]; + cvatom[i3][6] += a3[1] * f3[0]; + cvatom[i3][7] += a3[2] * f3[0]; + cvatom[i3][8] += a3[2] * f3[1]; } if (newton_bond || i4 < nlocal) { double a4[3]; // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4 - a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x); - a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y); - a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z); + a4[0] = 0.25 * (-vb1x + 2 * vb2x + 3 * vb3x); + a4[1] = 0.25 * (-vb1y + 2 * vb2y + 3 * vb3y); + a4[2] = 0.25 * (-vb1z + 2 * vb2z + 3 * vb3z); - cvatom[i4][0] += a4[0]*f4[0]; - cvatom[i4][1] += a4[1]*f4[1]; - cvatom[i4][2] += a4[2]*f4[2]; - cvatom[i4][3] += a4[0]*f4[1]; - cvatom[i4][4] += a4[0]*f4[2]; - cvatom[i4][5] += a4[1]*f4[2]; - cvatom[i4][6] += a4[1]*f4[0]; - cvatom[i4][7] += a4[2]*f4[0]; - cvatom[i4][8] += a4[2]*f4[1]; + cvatom[i4][0] += a4[0] * f4[0]; + cvatom[i4][1] += a4[1] * f4[1]; + cvatom[i4][2] += a4[2] * f4[2]; + cvatom[i4][3] += a4[0] * f4[1]; + cvatom[i4][4] += a4[0] * f4[2]; + cvatom[i4][5] += a4[1] * f4[2]; + cvatom[i4][6] += a4[1] * f4[0]; + cvatom[i4][7] += a4[2] * f4[0]; + cvatom[i4][8] += a4[2] * f4[1]; } } } /* ---------------------------------------------------------------------- */ -void Dihedral::problem(const char *filename, int lineno, - int i1, int i2, int i3, int i4) +void Dihedral::problem(const char *filename, int lineno, int i1, int i2, int i3, int i4) { const auto x = atom->x; - auto warn = fmt::format("Dihedral problem: {} {} {} {} {} {}\n", - comm->me, update->ntimestep, atom->tag[i1], - atom->tag[i2], atom->tag[i3], atom->tag[i4]); - warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i1][0],x[i1][1],x[i1][2]); - warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i2][0],x[i2][1],x[i2][2]); - warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i3][0],x[i3][1],x[i3][2]); - warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", - comm->me,x[i4][0],x[i4][1],x[i4][2]); + auto warn = fmt::format("Dihedral problem: {} {} {} {} {} {}\n", comm->me, update->ntimestep, + atom->tag[i1], atom->tag[i2], atom->tag[i3], atom->tag[i4]); + warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i1][0], x[i1][1], + x[i1][2]); + warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i2][0], x[i2][1], + x[i2][2]); + warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i3][0], x[i3][1], + x[i3][2]); + warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", comm->me, x[i4][0], x[i4][1], + x[i4][2]); error->warning(filename, lineno, warn); } @@ -412,8 +406,8 @@ void Dihedral::problem(const char *filename, int lineno, double Dihedral::memory_usage() { - double bytes = (double)comm->nthreads*maxeatom * sizeof(double); - bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double); - bytes += (double)comm->nthreads*maxcvatom*9 * sizeof(double); + double bytes = (double) comm->nthreads * maxeatom * sizeof(double); + bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double); + bytes += (double) comm->nthreads * maxcvatom * 9 * sizeof(double); return bytes; } diff --git a/src/improper.cpp b/src/improper.cpp index 00033880f0..7ba39368b7 100644 --- a/src/improper.cpp +++ b/src/improper.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -27,7 +26,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Improper::Improper(LAMMPS *lmp) : Pointers(lmp) +Improper::Improper(LAMMPS *_lmp) : Pointers(_lmp) { energy = 0.0; writedata = 0; @@ -66,10 +65,9 @@ Improper::~Improper() void Improper::init() { - if (!allocated && atom->nimpropertypes) - error->all(FLERR,"Improper coeffs are not set"); + if (!allocated && atom->nimpropertypes) error->all(FLERR, "Improper coeffs are not set"); for (int i = 1; i <= atom->nimpropertypes; i++) - if (setflag[i] == 0) error->all(FLERR,"All improper coeffs are not set"); + if (setflag[i] == 0) error->all(FLERR, "All improper coeffs are not set"); init_style(); } @@ -93,7 +91,7 @@ void Improper::init() void Improper::ev_setup(int eflag, int vflag, int alloc) { - int i,n; + int i, n; evflag = 1; @@ -103,11 +101,9 @@ void Improper::ev_setup(int eflag, int vflag, int alloc) vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR); vflag_atom = vflag & VIRIAL_ATOM; - if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) - vflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL) vflag_atom = 1; cvflag_atom = 0; - if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) - cvflag_atom = 1; + if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) cvflag_atom = 1; vflag_either = vflag_global || vflag_atom || cvflag_atom; // reallocate per-atom arrays if necessary @@ -116,28 +112,29 @@ void Improper::ev_setup(int eflag, int vflag, int alloc) maxeatom = atom->nmax; if (alloc) { memory->destroy(eatom); - memory->create(eatom,comm->nthreads*maxeatom,"improper:eatom"); + memory->create(eatom, comm->nthreads * maxeatom, "improper:eatom"); } } if (vflag_atom && atom->nmax > maxvatom) { maxvatom = atom->nmax; if (alloc) { memory->destroy(vatom); - memory->create(vatom,comm->nthreads*maxvatom,6,"improper:vatom"); + memory->create(vatom, comm->nthreads * maxvatom, 6, "improper:vatom"); } } if (cvflag_atom && atom->nmax > maxcvatom) { maxcvatom = atom->nmax; if (alloc) { memory->destroy(cvatom); - memory->create(cvatom,comm->nthreads*maxcvatom,9,"improper:cvatom"); + memory->create(cvatom, comm->nthreads * maxcvatom, 9, "improper:cvatom"); } } // zero accumulators if (eflag_global) energy = 0.0; - if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0; + if (vflag_global) + for (i = 0; i < 6; i++) virial[i] = 0.0; if (eflag_atom && alloc) { n = atom->nlocal; if (force->newton_bond) n += atom->nghost; @@ -180,20 +177,19 @@ void Improper::ev_setup(int eflag, int vflag, int alloc) = vb1*f1 + vb2*f3 + (vb3+vb2)*f4 ------------------------------------------------------------------------- */ -void Improper::ev_tally(int i1, int i2, int i3, int i4, - int nlocal, int newton_bond, - double eimproper, double *f1, double *f3, double *f4, - double vb1x, double vb1y, double vb1z, - double vb2x, double vb2y, double vb2z, +void Improper::ev_tally(int i1, int i2, int i3, int i4, int nlocal, int newton_bond, + double eimproper, double *f1, double *f3, double *f4, double vb1x, + double vb1y, double vb1z, double vb2x, double vb2y, double vb2z, double vb3x, double vb3y, double vb3z) { - double eimproperquarter,v[6]; + double eimproperquarter, v[6]; if (eflag_either) { if (eflag_global) { - if (newton_bond) energy += eimproper; + if (newton_bond) + energy += eimproper; else { - eimproperquarter = 0.25*eimproper; + eimproperquarter = 0.25 * eimproper; if (i1 < nlocal) energy += eimproperquarter; if (i2 < nlocal) energy += eimproperquarter; if (i3 < nlocal) energy += eimproperquarter; @@ -201,7 +197,7 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4, } } if (eflag_atom) { - eimproperquarter = 0.25*eimproper; + eimproperquarter = 0.25 * eimproper; if (newton_bond || i1 < nlocal) eatom[i1] += eimproperquarter; if (newton_bond || i2 < nlocal) eatom[i2] += eimproperquarter; if (newton_bond || i3 < nlocal) eatom[i3] += eimproperquarter; @@ -210,12 +206,12 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4, } if (vflag_either) { - v[0] = vb1x*f1[0] + vb2x*f3[0] + (vb3x+vb2x)*f4[0]; - v[1] = vb1y*f1[1] + vb2y*f3[1] + (vb3y+vb2y)*f4[1]; - v[2] = vb1z*f1[2] + vb2z*f3[2] + (vb3z+vb2z)*f4[2]; - v[3] = vb1x*f1[1] + vb2x*f3[1] + (vb3x+vb2x)*f4[1]; - v[4] = vb1x*f1[2] + vb2x*f3[2] + (vb3x+vb2x)*f4[2]; - v[5] = vb1y*f1[2] + vb2y*f3[2] + (vb3y+vb2y)*f4[2]; + v[0] = vb1x * f1[0] + vb2x * f3[0] + (vb3x + vb2x) * f4[0]; + v[1] = vb1y * f1[1] + vb2y * f3[1] + (vb3y + vb2y) * f4[1]; + v[2] = vb1z * f1[2] + vb2z * f3[2] + (vb3z + vb2z) * f4[2]; + v[3] = vb1x * f1[1] + vb2x * f3[1] + (vb3x + vb2x) * f4[1]; + v[4] = vb1x * f1[2] + vb2x * f3[2] + (vb3x + vb2x) * f4[2]; + v[5] = vb1y * f1[2] + vb2y * f3[2] + (vb3y + vb2y) * f4[2]; if (vflag_global) { if (newton_bond) { @@ -227,72 +223,72 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4, virial[5] += v[5]; } else { if (i1 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i2 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i3 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } if (i4 < nlocal) { - virial[0] += 0.25*v[0]; - virial[1] += 0.25*v[1]; - virial[2] += 0.25*v[2]; - virial[3] += 0.25*v[3]; - virial[4] += 0.25*v[4]; - virial[5] += 0.25*v[5]; + virial[0] += 0.25 * v[0]; + virial[1] += 0.25 * v[1]; + virial[2] += 0.25 * v[2]; + virial[3] += 0.25 * v[3]; + virial[4] += 0.25 * v[4]; + virial[5] += 0.25 * v[5]; } } } if (vflag_atom) { if (newton_bond || i1 < nlocal) { - vatom[i1][0] += 0.25*v[0]; - vatom[i1][1] += 0.25*v[1]; - vatom[i1][2] += 0.25*v[2]; - vatom[i1][3] += 0.25*v[3]; - vatom[i1][4] += 0.25*v[4]; - vatom[i1][5] += 0.25*v[5]; + vatom[i1][0] += 0.25 * v[0]; + vatom[i1][1] += 0.25 * v[1]; + vatom[i1][2] += 0.25 * v[2]; + vatom[i1][3] += 0.25 * v[3]; + vatom[i1][4] += 0.25 * v[4]; + vatom[i1][5] += 0.25 * v[5]; } if (newton_bond || i2 < nlocal) { - vatom[i2][0] += 0.25*v[0]; - vatom[i2][1] += 0.25*v[1]; - vatom[i2][2] += 0.25*v[2]; - vatom[i2][3] += 0.25*v[3]; - vatom[i2][4] += 0.25*v[4]; - vatom[i2][5] += 0.25*v[5]; + vatom[i2][0] += 0.25 * v[0]; + vatom[i2][1] += 0.25 * v[1]; + vatom[i2][2] += 0.25 * v[2]; + vatom[i2][3] += 0.25 * v[3]; + vatom[i2][4] += 0.25 * v[4]; + vatom[i2][5] += 0.25 * v[5]; } if (newton_bond || i3 < nlocal) { - vatom[i3][0] += 0.25*v[0]; - vatom[i3][1] += 0.25*v[1]; - vatom[i3][2] += 0.25*v[2]; - vatom[i3][3] += 0.25*v[3]; - vatom[i3][4] += 0.25*v[4]; - vatom[i3][5] += 0.25*v[5]; + vatom[i3][0] += 0.25 * v[0]; + vatom[i3][1] += 0.25 * v[1]; + vatom[i3][2] += 0.25 * v[2]; + vatom[i3][3] += 0.25 * v[3]; + vatom[i3][4] += 0.25 * v[4]; + vatom[i3][5] += 0.25 * v[5]; } if (newton_bond || i4 < nlocal) { - vatom[i4][0] += 0.25*v[0]; - vatom[i4][1] += 0.25*v[1]; - vatom[i4][2] += 0.25*v[2]; - vatom[i4][3] += 0.25*v[3]; - vatom[i4][4] += 0.25*v[4]; - vatom[i4][5] += 0.25*v[5]; + vatom[i4][0] += 0.25 * v[0]; + vatom[i4][1] += 0.25 * v[1]; + vatom[i4][2] += 0.25 * v[2]; + vatom[i4][3] += 0.25 * v[3]; + vatom[i4][4] += 0.25 * v[4]; + vatom[i4][5] += 0.25 * v[5]; } } } @@ -311,100 +307,97 @@ void Improper::ev_tally(int i1, int i2, int i3, int i4, double a1[3]; // a1 = r10 = (3*r12 - 2*r32 - r43)/4 - a1[0] = 0.25*(3*vb1x - 2*vb2x - vb3x); - a1[1] = 0.25*(3*vb1y - 2*vb2y - vb3y); - a1[2] = 0.25*(3*vb1z - 2*vb2z - vb3z); + a1[0] = 0.25 * (3 * vb1x - 2 * vb2x - vb3x); + a1[1] = 0.25 * (3 * vb1y - 2 * vb2y - vb3y); + a1[2] = 0.25 * (3 * vb1z - 2 * vb2z - vb3z); - cvatom[i1][0] += a1[0]*f1[0]; - cvatom[i1][1] += a1[1]*f1[1]; - cvatom[i1][2] += a1[2]*f1[2]; - cvatom[i1][3] += a1[0]*f1[1]; - cvatom[i1][4] += a1[0]*f1[2]; - cvatom[i1][5] += a1[1]*f1[2]; - cvatom[i1][6] += a1[1]*f1[0]; - cvatom[i1][7] += a1[2]*f1[0]; - cvatom[i1][8] += a1[2]*f1[1]; + cvatom[i1][0] += a1[0] * f1[0]; + cvatom[i1][1] += a1[1] * f1[1]; + cvatom[i1][2] += a1[2] * f1[2]; + cvatom[i1][3] += a1[0] * f1[1]; + cvatom[i1][4] += a1[0] * f1[2]; + cvatom[i1][5] += a1[1] * f1[2]; + cvatom[i1][6] += a1[1] * f1[0]; + cvatom[i1][7] += a1[2] * f1[0]; + cvatom[i1][8] += a1[2] * f1[1]; } if (newton_bond || i2 < nlocal) { double a2[3]; double f2[3]; // a2 = r20 = ( -r12 - 2*r32 - r43)/4 - a2[0] = 0.25*(-vb1x - 2*vb2x - vb3x); - a2[1] = 0.25*(-vb1y - 2*vb2y - vb3y); - a2[2] = 0.25*(-vb1z - 2*vb2z - vb3z); + a2[0] = 0.25 * (-vb1x - 2 * vb2x - vb3x); + a2[1] = 0.25 * (-vb1y - 2 * vb2y - vb3y); + a2[2] = 0.25 * (-vb1z - 2 * vb2z - vb3z); - f2[0] = - f1[0] - f3[0] - f4[0]; - f2[1] = - f1[1] - f3[1] - f4[1]; - f2[2] = - f1[2] - f3[2] - f4[2]; + f2[0] = -f1[0] - f3[0] - f4[0]; + f2[1] = -f1[1] - f3[1] - f4[1]; + f2[2] = -f1[2] - f3[2] - f4[2]; - cvatom[i2][0] += a2[0]*f2[0]; - cvatom[i2][1] += a2[1]*f2[1]; - cvatom[i2][2] += a2[2]*f2[2]; - cvatom[i2][3] += a2[0]*f2[1]; - cvatom[i2][4] += a2[0]*f2[2]; - cvatom[i2][5] += a2[1]*f2[2]; - cvatom[i2][6] += a2[1]*f2[0]; - cvatom[i2][7] += a2[2]*f2[0]; - cvatom[i2][8] += a2[2]*f2[1]; + cvatom[i2][0] += a2[0] * f2[0]; + cvatom[i2][1] += a2[1] * f2[1]; + cvatom[i2][2] += a2[2] * f2[2]; + cvatom[i2][3] += a2[0] * f2[1]; + cvatom[i2][4] += a2[0] * f2[2]; + cvatom[i2][5] += a2[1] * f2[2]; + cvatom[i2][6] += a2[1] * f2[0]; + cvatom[i2][7] += a2[2] * f2[0]; + cvatom[i2][8] += a2[2] * f2[1]; } if (newton_bond || i3 < nlocal) { double a3[3]; // a3 = r30 = ( -r12 + 2*r32 - r43)/4 - a3[0] = 0.25*(-vb1x + 2*vb2x - vb3x); - a3[1] = 0.25*(-vb1y + 2*vb2y - vb3y); - a3[2] = 0.25*(-vb1z + 2*vb2z - vb3z); + a3[0] = 0.25 * (-vb1x + 2 * vb2x - vb3x); + a3[1] = 0.25 * (-vb1y + 2 * vb2y - vb3y); + a3[2] = 0.25 * (-vb1z + 2 * vb2z - vb3z); - cvatom[i3][0] += a3[0]*f3[0]; - cvatom[i3][1] += a3[1]*f3[1]; - cvatom[i3][2] += a3[2]*f3[2]; - cvatom[i3][3] += a3[0]*f3[1]; - cvatom[i3][4] += a3[0]*f3[2]; - cvatom[i3][5] += a3[1]*f3[2]; - cvatom[i3][6] += a3[1]*f3[0]; - cvatom[i3][7] += a3[2]*f3[0]; - cvatom[i3][8] += a3[2]*f3[1]; + cvatom[i3][0] += a3[0] * f3[0]; + cvatom[i3][1] += a3[1] * f3[1]; + cvatom[i3][2] += a3[2] * f3[2]; + cvatom[i3][3] += a3[0] * f3[1]; + cvatom[i3][4] += a3[0] * f3[2]; + cvatom[i3][5] += a3[1] * f3[2]; + cvatom[i3][6] += a3[1] * f3[0]; + cvatom[i3][7] += a3[2] * f3[0]; + cvatom[i3][8] += a3[2] * f3[1]; } if (newton_bond || i4 < nlocal) { double a4[3]; // a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4 - a4[0] = 0.25*(-vb1x + 2*vb2x + 3*vb3x); - a4[1] = 0.25*(-vb1y + 2*vb2y + 3*vb3y); - a4[2] = 0.25*(-vb1z + 2*vb2z + 3*vb3z); + a4[0] = 0.25 * (-vb1x + 2 * vb2x + 3 * vb3x); + a4[1] = 0.25 * (-vb1y + 2 * vb2y + 3 * vb3y); + a4[2] = 0.25 * (-vb1z + 2 * vb2z + 3 * vb3z); - cvatom[i4][0] += a4[0]*f4[0]; - cvatom[i4][1] += a4[1]*f4[1]; - cvatom[i4][2] += a4[2]*f4[2]; - cvatom[i4][3] += a4[0]*f4[1]; - cvatom[i4][4] += a4[0]*f4[2]; - cvatom[i4][5] += a4[1]*f4[2]; - cvatom[i4][6] += a4[1]*f4[0]; - cvatom[i4][7] += a4[2]*f4[0]; - cvatom[i4][8] += a4[2]*f4[1]; + cvatom[i4][0] += a4[0] * f4[0]; + cvatom[i4][1] += a4[1] * f4[1]; + cvatom[i4][2] += a4[2] * f4[2]; + cvatom[i4][3] += a4[0] * f4[1]; + cvatom[i4][4] += a4[0] * f4[2]; + cvatom[i4][5] += a4[1] * f4[2]; + cvatom[i4][6] += a4[1] * f4[0]; + cvatom[i4][7] += a4[2] * f4[0]; + cvatom[i4][8] += a4[2] * f4[1]; } } } /* ---------------------------------------------------------------------- */ - -void Improper::problem(const char *filename, int lineno, - int i1, int i2, int i3, int i4) +void Improper::problem(const char *filename, int lineno, int i1, int i2, int i3, int i4) { const auto x = atom->x; - auto warn = fmt::format("Improper problem: {} {} {} {} {} {}\n", - comm->me, update->ntimestep, atom->tag[i1], - atom->tag[i2], atom->tag[i3], atom->tag[i4]); - warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i1][0],x[i1][1],x[i1][2]); - warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i2][0],x[i2][1],x[i2][2]); - warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", - comm->me,x[i3][0],x[i3][1],x[i3][2]); - warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", - comm->me,x[i4][0],x[i4][1],x[i4][2]); + auto warn = fmt::format("Improper problem: {} {} {} {} {} {}\n", comm->me, update->ntimestep, + atom->tag[i1], atom->tag[i2], atom->tag[i3], atom->tag[i4]); + warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i1][0], x[i1][1], + x[i1][2]); + warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i2][0], x[i2][1], + x[i2][2]); + warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i3][0], x[i3][1], + x[i3][2]); + warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", comm->me, x[i4][0], x[i4][1], + x[i4][2]); error->warning(filename, lineno, warn); } @@ -412,7 +405,7 @@ void Improper::problem(const char *filename, int lineno, double Improper::memory_usage() { - double bytes = (double)comm->nthreads*maxeatom * sizeof(double); - bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double); + double bytes = (double) comm->nthreads * maxeatom * sizeof(double); + bytes += (double) comm->nthreads * maxvatom * 6 * sizeof(double); return bytes; } diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index bfbd466ae8..c3ff91d6a8 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -1,4 +1,3 @@ -// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -22,15 +21,14 @@ using namespace LAMMPS_NS; -TableFileReader::TableFileReader(LAMMPS *lmp, - const std::string &filename, - const std::string &type, +TableFileReader::TableFileReader(LAMMPS *lmp, const std::string &filename, const std::string &type, const int auto_convert) : - PotentialFileReader(lmp, filename, type + " table", auto_convert) + PotentialFileReader(lmp, filename, type + " table", auto_convert) { } -char *TableFileReader::find_section_start(const std::string &keyword) { +char *TableFileReader::find_section_start(const std::string &keyword) +{ char *line = nullptr; while ((line = reader->next_line())) { ValueTokenizer values(line); diff --git a/src/timer.cpp b/src/timer.cpp index 0cbf687137..785d345512 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -24,10 +23,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Timer::Timer(LAMMPS *lmp) : Pointers(lmp) +Timer::Timer(LAMMPS *_lmp) : Pointers(_lmp) { _level = NORMAL; - _sync = OFF; + _sync = OFF; _timeout = -1; _s_timeout = -1; _checkfreq = 10; @@ -49,7 +48,7 @@ void Timer::init() void Timer::_stamp(enum ttype which) { - double current_cpu=0.0, current_wall=0.0; + double current_cpu = 0.0, current_wall = 0.0; if (_level > NORMAL) current_cpu = platform::cputime(); current_wall = platform::walltime(); @@ -58,13 +57,13 @@ void Timer::_stamp(enum ttype which) const double delta_cpu = current_cpu - previous_cpu; const double delta_wall = current_wall - previous_wall; - cpu_array[which] += delta_cpu; + cpu_array[which] += delta_cpu; wall_array[which] += delta_wall; - cpu_array[ALL] += delta_cpu; - wall_array[ALL] += delta_wall; + cpu_array[ALL] += delta_cpu; + wall_array[ALL] += delta_wall; } - previous_cpu = current_cpu; + previous_cpu = current_cpu; previous_wall = current_wall; if (which == RESET) { @@ -78,9 +77,9 @@ void Timer::_stamp(enum ttype which) if (_level > NORMAL) current_cpu = platform::cputime(); current_wall = platform::walltime(); - cpu_array[SYNC] += current_cpu - previous_cpu; + cpu_array[SYNC] += current_cpu - previous_cpu; wall_array[SYNC] += current_wall - previous_wall; - previous_cpu = current_cpu; + previous_cpu = current_cpu; previous_wall = current_wall; } } @@ -89,7 +88,7 @@ void Timer::_stamp(enum ttype which) void Timer::barrier_start() { - double current_cpu=0.0, current_wall=0.0; + double current_cpu = 0.0, current_wall = 0.0; MPI_Barrier(world); @@ -98,9 +97,9 @@ void Timer::barrier_start() current_cpu = platform::cputime(); current_wall = platform::walltime(); - cpu_array[TOTAL] = current_cpu; + cpu_array[TOTAL] = current_cpu; wall_array[TOTAL] = current_wall; - previous_cpu = current_cpu; + previous_cpu = current_cpu; previous_wall = current_wall; } @@ -108,7 +107,7 @@ void Timer::barrier_start() void Timer::barrier_stop() { - double current_cpu=0.0, current_wall=0.0; + double current_cpu = 0.0, current_wall = 0.0; MPI_Barrier(world); @@ -117,7 +116,7 @@ void Timer::barrier_stop() current_cpu = platform::cputime(); current_wall = platform::walltime(); - cpu_array[TOTAL] = current_cpu - cpu_array[TOTAL]; + cpu_array[TOTAL] = current_cpu - cpu_array[TOTAL]; wall_array[TOTAL] = current_wall - wall_array[TOTAL]; } @@ -169,14 +168,13 @@ void Timer::print_timeout(FILE *fp) // remaining timeout in seconds int s = _timeout - d; // remaining 1/100ths of seconds - const int hs = 100*((_timeout - d) - s); + const int hs = 100 * ((_timeout - d) - s); // breaking s down into second/minutes/hours const int seconds = s % 60; - s = (s - seconds) / 60; + s = (s - seconds) / 60; const int minutes = s % 60; const int hours = (s - minutes) / 60; - fprintf(fp," Walltime left : %d:%02d:%02d.%02d\n", - hours,minutes,seconds,hs); + fprintf(fp, " Walltime left : %d:%02d:%02d.%02d\n", hours, minutes, seconds, hs); } } @@ -186,14 +184,13 @@ bool Timer::_check_timeout() { double walltime = platform::walltime() - timeout_start; // broadcast time to insure all ranks act the same. - MPI_Bcast(&walltime,1,MPI_DOUBLE,0,world); + MPI_Bcast(&walltime, 1, MPI_DOUBLE, 0, world); if (walltime < _timeout) { _nextcheck += _checkfreq; return false; } else { - if (comm->me == 0) - error->warning(FLERR,"Wall time limit reached"); + if (comm->me == 0) error->warning(FLERR, "Wall time limit reached"); _timeout = 0.0; return true; } @@ -208,38 +205,40 @@ double Timer::get_timeout_remain() /* ---------------------------------------------------------------------- modify parameters of the Timer class ------------------------------------------------------------------------- */ -static const char *timer_style[] = { "off", "loop", "normal", "full" }; -static const char *timer_mode[] = { "nosync", "(dummy)", "sync" }; +static const char *timer_style[] = {"off", "loop", "normal", "full"}; +static const char *timer_mode[] = {"nosync", "(dummy)", "sync"}; void Timer::modify_params(int narg, char **arg) { int iarg = 0; while (iarg < narg) { - if (strcmp(arg[iarg],timer_style[OFF]) == 0) { + if (strcmp(arg[iarg], timer_style[OFF]) == 0) { _level = OFF; - } else if (strcmp(arg[iarg],timer_style[LOOP]) == 0) { + } else if (strcmp(arg[iarg], timer_style[LOOP]) == 0) { _level = LOOP; - } else if (strcmp(arg[iarg],timer_style[NORMAL]) == 0) { + } else if (strcmp(arg[iarg], timer_style[NORMAL]) == 0) { _level = NORMAL; - } else if (strcmp(arg[iarg],timer_style[FULL]) == 0) { + } else if (strcmp(arg[iarg], timer_style[FULL]) == 0) { _level = FULL; - } else if (strcmp(arg[iarg],timer_mode[OFF]) == 0) { - _sync = OFF; - } else if (strcmp(arg[iarg],timer_mode[NORMAL]) == 0) { - _sync = NORMAL; - } else if (strcmp(arg[iarg],"timeout") == 0) { + } else if (strcmp(arg[iarg], timer_mode[OFF]) == 0) { + _sync = OFF; + } else if (strcmp(arg[iarg], timer_mode[NORMAL]) == 0) { + _sync = NORMAL; + } else if (strcmp(arg[iarg], "timeout") == 0) { ++iarg; if (iarg < narg) { _timeout = utils::timespec2seconds(arg[iarg]); - } else error->all(FLERR,"Illegal timer command"); - } else if (strcmp(arg[iarg],"every") == 0) { + } else + error->all(FLERR, "Illegal timer command"); + } else if (strcmp(arg[iarg], "every") == 0) { ++iarg; if (iarg < narg) { - _checkfreq = utils::inumeric(FLERR,arg[iarg],false,lmp); - if (_checkfreq <= 0) - error->all(FLERR,"Illegal timer command"); - } else error->all(FLERR,"Illegal timer command"); - } else error->all(FLERR,"Illegal timer command"); + _checkfreq = utils::inumeric(FLERR, arg[iarg], false, lmp); + if (_checkfreq <= 0) error->all(FLERR, "Illegal timer command"); + } else + error->all(FLERR, "Illegal timer command"); + } else + error->all(FLERR, "Illegal timer command"); ++iarg; } @@ -253,7 +252,7 @@ void Timer::modify_params(int narg, char **arg) timeout = fmt::format("{:%H:%M:%S}", fmt::gmtime(tv)); } - utils::logmesg(lmp,"New timer settings: style={} mode={} timeout={}\n", - timer_style[_level],timer_mode[_sync],timeout); + utils::logmesg(lmp, "New timer settings: style={} mode={} timeout={}\n", timer_style[_level], + timer_mode[_sync], timeout); } } diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index 35a313ab3d..89c5b99dfb 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -1,4 +1,3 @@ -// clang-format off /* -*- c++ -*- ---------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -17,19 +16,20 @@ ------------------------------------------------------------------------- */ #include "tokenizer.h" -#include "utils.h" #include "fmt/format.h" +#include "utils.h" #include using namespace LAMMPS_NS; -TokenizerException::TokenizerException(const std::string &msg, const std::string &token) { - if (token.empty()) { - message = msg; - } else { - message = fmt::format("{}: '{}'", msg, token); - } +TokenizerException::TokenizerException(const std::string &msg, const std::string &token) +{ + if (token.empty()) { + message = msg; + } else { + message = fmt::format("{}: '{}'", msg, token); + } } /** Class for splitting text into words @@ -52,117 +52,122 @@ TokenizerException::TokenizerException(const std::string &msg, const std::string Tokenizer::Tokenizer(std::string str, std::string _separators) : text(std::move(str)), separators(std::move(_separators)), start(0), ntokens(std::string::npos) { - // replace known UTF-8 characters with ASCII equivalents - if (utils::has_utf8(text)) text = utils::utf8_subst(text); - reset(); + // replace known UTF-8 characters with ASCII equivalents + if (utils::has_utf8(text)) text = utils::utf8_subst(text); + reset(); } Tokenizer::Tokenizer(const Tokenizer &rhs) : text(rhs.text), separators(rhs.separators), ntokens(rhs.ntokens) { - reset(); + reset(); } -Tokenizer::Tokenizer(Tokenizer && rhs) : +Tokenizer::Tokenizer(Tokenizer &&rhs) : text(std::move(rhs.text)), separators(std::move(rhs.separators)), ntokens(rhs.ntokens) { - reset(); + reset(); } -Tokenizer& Tokenizer::operator=(const Tokenizer& other) +Tokenizer &Tokenizer::operator=(const Tokenizer &other) { - Tokenizer tmp(other); - swap(tmp); - return *this; + Tokenizer tmp(other); + swap(tmp); + return *this; } -Tokenizer& Tokenizer::operator=(Tokenizer&& other) +Tokenizer &Tokenizer::operator=(Tokenizer &&other) { - Tokenizer tmp(std::move(other)); - swap(tmp); - return *this; + Tokenizer tmp(std::move(other)); + swap(tmp); + return *this; } -void Tokenizer::swap(Tokenizer& other) +void Tokenizer::swap(Tokenizer &other) { - std::swap(text, other.text); - std::swap(separators, other.separators); - std::swap(start, other.start); - std::swap(ntokens, other.ntokens); + std::swap(text, other.text); + std::swap(separators, other.separators); + std::swap(start, other.start); + std::swap(ntokens, other.ntokens); } /*! Re-position the tokenizer state to the first word, * i.e. the first non-separator character */ -void Tokenizer::reset() { - start = text.find_first_not_of(separators); +void Tokenizer::reset() +{ + start = text.find_first_not_of(separators); } /*! Search the text to be processed for a sub-string. * * \param str string to be searched for * \return true if string was found, false if not */ -bool Tokenizer::contains(const std::string &str) const { - return text.find(str) != std::string::npos; +bool Tokenizer::contains(const std::string &str) const +{ + return text.find(str) != std::string::npos; } /*! Skip over a given number of tokens * * \param n number of tokens to skip over */ -void Tokenizer::skip(int n) { - for (int i = 0; i < n; ++i) { - if (!has_next()) throw TokenizerException("No more tokens", ""); - - size_t end = text.find_first_of(separators, start); - - if (end == std::string::npos) { - start = end; - } else { - start = text.find_first_not_of(separators, end+1); - } - } -} - -/*! Indicate whether more tokens are available - * - * \return true if there are more tokens, false if not */ -bool Tokenizer::has_next() const { - return start != std::string::npos; -} - -/*! Retrieve next token. - * - * \return string with the next token */ -std::string Tokenizer::next() { +void Tokenizer::skip(int n) +{ + for (int i = 0; i < n; ++i) { if (!has_next()) throw TokenizerException("No more tokens", ""); size_t end = text.find_first_of(separators, start); if (end == std::string::npos) { - std::string token = text.substr(start); - start = end; - return token; + start = end; + } else { + start = text.find_first_not_of(separators, end + 1); } + } +} - std::string token = text.substr(start, end-start); - start = text.find_first_not_of(separators, end+1); +/*! Indicate whether more tokens are available + * + * \return true if there are more tokens, false if not */ +bool Tokenizer::has_next() const +{ + return start != std::string::npos; +} + +/*! Retrieve next token. + * + * \return string with the next token */ +std::string Tokenizer::next() +{ + if (!has_next()) throw TokenizerException("No more tokens", ""); + + size_t end = text.find_first_of(separators, start); + + if (end == std::string::npos) { + std::string token = text.substr(start); + start = end; return token; + } + + std::string token = text.substr(start, end - start); + start = text.find_first_not_of(separators, end + 1); + return token; } /*! Count number of tokens in text. * * \return number of counted tokens */ -size_t Tokenizer::count() { - // lazy evaluation - if (ntokens == std::string::npos) { - ntokens = utils::count_words(text, separators); - } - return ntokens; +size_t Tokenizer::count() +{ + // lazy evaluation + if (ntokens == std::string::npos) { ntokens = utils::count_words(text, separators); } + return ntokens; } /*! Retrieve the entire text converted to an STL vector of tokens. * * \return The STL vector */ -std::vector Tokenizer::as_vector() { +std::vector Tokenizer::as_vector() +{ // store current state size_t current = start; @@ -171,9 +176,7 @@ std::vector Tokenizer::as_vector() { // generate vector std::vector tokens; - while (has_next()) { - tokens.emplace_back(next()); - } + while (has_next()) { tokens.emplace_back(next()); } // restore state start = current; @@ -195,107 +198,109 @@ std::vector Tokenizer::as_vector() { * * \see Tokenizer InvalidIntegerException InvalidFloatException */ -ValueTokenizer::ValueTokenizer(const std::string &str, const std::string &separators) : tokens(str, separators) { -} - -ValueTokenizer::ValueTokenizer(ValueTokenizer &&rhs) : tokens(std::move(rhs.tokens)) { -} - -ValueTokenizer& ValueTokenizer::operator=(const ValueTokenizer& other) +ValueTokenizer::ValueTokenizer(const std::string &str, const std::string &separators) : + tokens(str, separators) { - ValueTokenizer tmp(other); - swap(tmp); - return *this; } -ValueTokenizer& ValueTokenizer::operator=(ValueTokenizer&& other) +ValueTokenizer::ValueTokenizer(ValueTokenizer &&rhs) : tokens(std::move(rhs.tokens)) {} + +ValueTokenizer &ValueTokenizer::operator=(const ValueTokenizer &other) { - ValueTokenizer tmp(std::move(other)); - swap(tmp); - return *this; + ValueTokenizer tmp(other); + swap(tmp); + return *this; } -void ValueTokenizer::swap(ValueTokenizer& other) +ValueTokenizer &ValueTokenizer::operator=(ValueTokenizer &&other) { - std::swap(tokens, other.tokens); + ValueTokenizer tmp(std::move(other)); + swap(tmp); + return *this; +} + +void ValueTokenizer::swap(ValueTokenizer &other) +{ + std::swap(tokens, other.tokens); } /*! Indicate whether more tokens are available * * \return true if there are more tokens, false if not */ -bool ValueTokenizer::has_next() const { - return tokens.has_next(); +bool ValueTokenizer::has_next() const +{ + return tokens.has_next(); } /*! Search the text to be processed for a sub-string. * * \param value string with value to be searched for * \return true if string was found, false if not */ -bool ValueTokenizer::contains(const std::string &value) const { - return tokens.contains(value); +bool ValueTokenizer::contains(const std::string &value) const +{ + return tokens.contains(value); } /*! Retrieve next token * * \return string with next token */ -std::string ValueTokenizer::next_string() { - return tokens.next(); +std::string ValueTokenizer::next_string() +{ + return tokens.next(); } /*! Retrieve next token and convert to int * * \return value of next token */ -int ValueTokenizer::next_int() { - std::string current = tokens.next(); - if (!utils::is_integer(current)) { - throw InvalidIntegerException(current); - } - return atoi(current.c_str()); +int ValueTokenizer::next_int() +{ + std::string current = tokens.next(); + if (!utils::is_integer(current)) { throw InvalidIntegerException(current); } + return atoi(current.c_str()); } /*! Retrieve next token and convert to bigint * * \return value of next token */ -bigint ValueTokenizer::next_bigint() { - std::string current = tokens.next(); - if (!utils::is_integer(current)) { - throw InvalidIntegerException(current); - } - return ATOBIGINT(current.c_str()); +bigint ValueTokenizer::next_bigint() +{ + std::string current = tokens.next(); + if (!utils::is_integer(current)) { throw InvalidIntegerException(current); } + return ATOBIGINT(current.c_str()); } /*! Retrieve next token and convert to tagint * * \return value of next token */ -tagint ValueTokenizer::next_tagint() { - std::string current = tokens.next(); - if (!utils::is_integer(current)) { - throw InvalidIntegerException(current); - } - return ATOTAGINT(current.c_str()); +tagint ValueTokenizer::next_tagint() +{ + std::string current = tokens.next(); + if (!utils::is_integer(current)) { throw InvalidIntegerException(current); } + return ATOTAGINT(current.c_str()); } /*! Retrieve next token and convert to double * * \return value of next token */ -double ValueTokenizer::next_double() { - std::string current = tokens.next(); - if (!utils::is_double(current)) { - throw InvalidFloatException(current); - } - return atof(current.c_str()); +double ValueTokenizer::next_double() +{ + std::string current = tokens.next(); + if (!utils::is_double(current)) { throw InvalidFloatException(current); } + return atof(current.c_str()); } /*! Skip over a given number of tokens * * \param n number of tokens to skip over */ -void ValueTokenizer::skip(int n) { - tokens.skip(n); +void ValueTokenizer::skip(int n) +{ + tokens.skip(n); } /*! Count number of tokens in text. * * \return number of counted tokens */ -size_t ValueTokenizer::count() { - return tokens.count(); +size_t ValueTokenizer::count() +{ + return tokens.count(); }