enable and apply clang-format

src/compute_dihedral.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -25,8 +24,7 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    Compute(lmp, narg, arg), emine(nullptr)
-  emine(nullptr)
 {
   if (narg != 3) error->all(FLERR, "Illegal compute dihedral command");
 
@@ -38,8 +36,7 @@ ComputeDihedral::ComputeDihedral(LAMMPS *lmp, int narg, char **arg) :
   // check if dihedral style hybrid exists
 
   dihedral = dynamic_cast<DihedralHybrid *>(force->dihedral_match("hybrid"));
-  if (!dihedral)
+  if (!dihedral) error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
-    error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
   size_vector = nsub = dihedral->nstyles;
 
   emine = new double[nsub];
@@ -61,8 +58,7 @@ void ComputeDihedral::init()
   // recheck dihedral style in case it has been changed
 
   dihedral = dynamic_cast<DihedralHybrid *>(force->dihedral_match("hybrid"));
-  if (!dihedral)
+  if (!dihedral) error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
-    error->all(FLERR, "Dihedral style for compute dihedral command is not hybrid");
   if (dihedral->nstyles != nsub)
     error->all(FLERR, "Dihedral style for compute dihedral command has changed");
 }
@@ -75,8 +71,7 @@ void ComputeDihedral::compute_vector()
   if (update->eflag_global != invoked_vector)
     error->all(FLERR, "Energy was not tallied on needed timestep");
 
-  for (int i = 0; i < nsub; i++)
+  for (int i = 0; i < nsub; i++) emine[i] = dihedral->styles[i]->energy;
-    emine[i] = dihedral->styles[i]->energy;
 
   MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
 }

src/compute_improper.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,19 +13,18 @@
 
 #include "compute_improper.h"
 
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "improper.h"
 #include "improper_hybrid.h"
-#include "error.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
 ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg),
+    Compute(lmp, narg, arg), emine(nullptr)
-  emine(nullptr)
 {
   if (narg != 3) error->all(FLERR, "Illegal compute improper command");
 
@@ -38,8 +36,7 @@ ComputeImproper::ComputeImproper(LAMMPS *lmp, int narg, char **arg) :
   // check if improper style hybrid exists
 
   improper = dynamic_cast<ImproperHybrid *>(force->improper_match("hybrid"));
-  if (!improper)
+  if (!improper) error->all(FLERR, "Improper style for compute improper command is not hybrid");
-    error->all(FLERR, "Improper style for compute improper command is not hybrid");
   size_vector = nsub = improper->nstyles;
 
   emine = new double[nsub];
@@ -61,8 +58,7 @@ void ComputeImproper::init()
   // recheck improper style in case it has been changed
 
   improper = dynamic_cast<ImproperHybrid *>(force->improper_match("hybrid"));
-  if (!improper)
+  if (!improper) error->all(FLERR, "Improper style for compute improper command is not hybrid");
-    error->all(FLERR, "Improper style for compute improper command is not hybrid");
   if (improper->nstyles != nsub)
     error->all(FLERR, "Improper style for compute improper command has changed");
 }
@@ -75,8 +71,7 @@ void ComputeImproper::compute_vector()
   if (update->eflag_global != invoked_vector)
     error->all(FLERR, "Energy was not tallied on needed timestep");
 
-  for (int i = 0; i < nsub; i++)
+  for (int i = 0; i < nsub; i++) emine[i] = improper->styles[i]->energy;
-    emine[i] = improper->styles[i]->energy;
 
   MPI_Allreduce(emine, vector, nsub, MPI_DOUBLE, MPI_SUM, world);
 }

src/fix_dummy.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -13,16 +12,16 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_dummy.h"
-#include <cstring>
 #include "error.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) :
+FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
-  Fix(lmp, narg, arg)
 {
   // process optional args
   // customize here and in setmask() by adding a new keyword from fix.h
@@ -39,14 +38,22 @@ FixDummy::FixDummy(LAMMPS *lmp, int narg, char **arg) :
 
   int iarg = 3;
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"initial_integrate") == 0) initial_integrate_flag = 1;
+    if (strcmp(arg[iarg], "initial_integrate") == 0)
-    else if (strcmp(arg[iarg],"final_integrate") == 0) final_integrate_flag = 1;
+      initial_integrate_flag = 1;
-    else if (strcmp(arg[iarg],"pre_exchange") == 0) pre_exchange_flag = 1;
+    else if (strcmp(arg[iarg], "final_integrate") == 0)
-    else if (strcmp(arg[iarg],"pre_neighbor") == 0) pre_neighbor_flag = 1;
+      final_integrate_flag = 1;
-    else if (strcmp(arg[iarg],"pre_force") == 0) pre_force_flag = 1;
+    else if (strcmp(arg[iarg], "pre_exchange") == 0)
-    else if (strcmp(arg[iarg],"post_force") == 0) post_force_flag = 1;
+      pre_exchange_flag = 1;
-    else if (strcmp(arg[iarg],"end_of_step") == 0) end_of_step_flag = 1;
+    else if (strcmp(arg[iarg], "pre_neighbor") == 0)
-    else error->all(FLERR,"Illegal fix DUMMY command");
+      pre_neighbor_flag = 1;
+    else if (strcmp(arg[iarg], "pre_force") == 0)
+      pre_force_flag = 1;
+    else if (strcmp(arg[iarg], "post_force") == 0)
+      post_force_flag = 1;
+    else if (strcmp(arg[iarg], "end_of_step") == 0)
+      end_of_step_flag = 1;
+    else
+      error->all(FLERR, "Illegal fix DUMMY command");
     iarg++;
   }
 }

src/fix_nve_noforce.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -24,8 +23,7 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixNVENoforce::FixNVENoforce(LAMMPS *lmp, int narg, char **arg) :
+FixNVENoforce::FixNVENoforce(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
-  Fix(lmp, narg, arg)
 {
   if (narg != 3) error->all(FLERR, "Illegal fix nve/noforce command");
 

src/fix_nvt_sphere.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -23,19 +22,15 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) :
+FixNVTSphere::FixNVTSphere(LAMMPS *lmp, int narg, char **arg) : FixNHSphere(lmp, narg, arg)
-  FixNHSphere(lmp, narg, arg)
 {
-  if (!tstat_flag)
+  if (!tstat_flag) error->all(FLERR, "Temperature control must be used with fix nvt/sphere");
-    error->all(FLERR,"Temperature control must be used with fix nvt/sphere");
+  if (pstat_flag) error->all(FLERR, "Pressure control can not be used with fix nvt/sphere");
-  if (pstat_flag)
-    error->all(FLERR,"Pressure control can not be used with fix nvt/sphere");
 
   // create a new compute temp style
   // id = fix-ID + temp
 
   id_temp = utils::strdup(std::string(id) + "_temp");
-  modify->add_compute(fmt::format("{} {} temp/sphere",
+  modify->add_compute(fmt::format("{} {} temp/sphere", id_temp, group->names[igroup]));
-                                  id_temp,group->names[igroup]));
   tcomputeflag = 1;
 }

src/fix_wall_harmonic.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -21,8 +20,7 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
+FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp, narg, arg)
-  FixWall(lmp, narg, arg)
 {
   dynamic_group_allow = 1;
 }
@@ -52,8 +50,10 @@ void FixWallHarmonic::wall_particle(int m, int which, double coord)
 
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) {
-      if (side < 0) delta = x[i][dim] - coord;
+      if (side < 0)
-      else delta = coord - x[i][dim];
+        delta = x[i][dim] - coord;
+      else
+        delta = coord - x[i][dim];
       if (delta >= cutoff[m]) continue;
       if (delta <= 0.0) {
         onflag = 1;
@@ -66,8 +66,10 @@ void FixWallHarmonic::wall_particle(int m, int which, double coord)
       ewall[m + 1] += fwall;
 
       if (evflag) {
-        if (side < 0) vn = -fwall*delta;
+        if (side < 0)
-        else vn = fwall*delta;
+          vn = -fwall * delta;
+        else
+          vn = fwall * delta;
         v_tally(dim, i, vn);
       }
     }

src/fix_wall_morse.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -13,17 +12,17 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_morse.h"
-#include <cmath>
 #include "atom.h"
 #include "error.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) :
+FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) : FixWall(lmp, narg, arg)
-  FixWall(lmp, narg, arg)
 {
   dynamic_group_allow = 1;
 }
@@ -62,8 +61,10 @@ void FixWallMorse::wall_particle(int m, int which, double coord)
 
   for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
-      if (side < 0) delta = x[i][dim] - coord;
+      if (side < 0)
-      else delta = coord - x[i][dim];
+        delta = x[i][dim] - coord;
+      else
+        delta = coord - x[i][dim];
       if (delta >= cutoff[m]) continue;
       if (delta <= 0.0) {
         onflag = 1;
@@ -77,8 +78,10 @@ void FixWallMorse::wall_particle(int m, int which, double coord)
       ewall[m + 1] += fwall;
 
       if (evflag) {
-        if (side < 0) vn = -fwall*delta;
+        if (side < 0)
-        else vn = fwall*delta;
+          vn = -fwall * delta;
+        else
+          vn = fwall * delta;
         v_tally(dim, i, vn);
       }
     }

src/npair_copy.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/npair_full_bin_atomonly.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -85,8 +84,7 @@ void NPairFullBinAtomonly::build(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     ipage->vgot(n);
-    if (ipage->status())
+    if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
 
   list->inum = inum;

src/npair_halffull_newtoff.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -74,8 +73,7 @@ void NPairHalffullNewtoff::build(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     ipage->vgot(n);
-    if (ipage->status())
+    if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
 
   list->inum = inum;

src/npair_skip_size.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -80,8 +79,7 @@ void NPairSkipSize::build(NeighList *list)
     firstneigh[i] = neighptr;
     numneigh[i] = n;
     ipage->vgot(n);
-    if (ipage->status())
+    if (ipage->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
-      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
   }
 
   list->inum = inum;

src/nstencil_full_bin_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -32,6 +31,5 @@ void NStencilFullBin2d::create()
 
   for (j = -sy; j <= sy; j++)
     for (i = -sx; i <= sx; i++)
-      if (bin_distance(i,j,0) < cutneighmaxsq)
+      if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
-        stencil[nstencil++] = j*mbinx + i;
 }

src/nstencil_full_bin_3d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_full_ghost_bin_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_full_ghost_bin_3d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_full_multi_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -50,7 +49,6 @@ void NStencilFullMulti2d::create()
   int n = ncollections;
   double cutsq;
 
-
   for (icollection = 0; icollection < n; icollection++) {
     for (jcollection = 0; jcollection < n; jcollection++) {
       if (flag_skip_multi[icollection][jcollection]) {

src/nstencil_full_multi_old_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_full_multi_old_3d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_half_bin_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -33,6 +32,5 @@ void NStencilHalfBin2d::create()
   for (j = 0; j <= sy; j++)
     for (i = -sx; i <= sx; i++)
       if (j > 0 || (j == 0 && i > 0))
-        if (bin_distance(i,j,0) < cutneighmaxsq)
+        if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
-          stencil[nstencil++] = j*mbinx + i;
 }

src/nstencil_half_bin_2d_tri.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -18,8 +17,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) :
+NStencilHalfBin2dTri::NStencilHalfBin2dTri(LAMMPS *lmp) : NStencil(lmp) {}
-  NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff
@@ -33,6 +31,5 @@ void NStencilHalfBin2dTri::create()
 
   for (j = 0; j <= sy; j++)
     for (i = -sx; i <= sx; i++)
-      if (bin_distance(i,j,0) < cutneighmaxsq)
+      if (bin_distance(i, j, 0) < cutneighmaxsq) stencil[nstencil++] = j * mbinx + i;
-        stencil[nstencil++] = j*mbinx + i;
 }

src/nstencil_half_bin_3d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories

src/nstencil_half_bin_3d_tri.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -18,8 +17,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) :
+NStencilHalfBin3dTri::NStencilHalfBin3dTri(LAMMPS *lmp) : NStencil(lmp) {}
-  NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff

src/nstencil_half_multi_old_2d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfMultiOld2d::
+NStencilHalfMultiOld2d::NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
-NStencilHalfMultiOld2d(LAMMPS *lmp) : NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff

src/nstencil_half_multi_old_2d_tri.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfMultiOld2dTri::
+NStencilHalfMultiOld2dTri::NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {}
-NStencilHalfMultiOld2dTri(LAMMPS *lmp) : NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff

src/nstencil_half_multi_old_3d.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfMultiOld3d::
+NStencilHalfMultiOld3d::NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
-NStencilHalfMultiOld3d(LAMMPS *lmp) : NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff

src/nstencil_half_multi_old_3d_tri.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -19,8 +18,7 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-NStencilHalfMultiOld3dTri::
+NStencilHalfMultiOld3dTri::NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {}
-NStencilHalfMultiOld3dTri(LAMMPS *lmp) : NStencil(lmp) {}
 
 /* ----------------------------------------------------------------------
    create stencil based on bin geometry and cutoff

src/ntopo_bond_all.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -15,14 +14,13 @@
 #include "ntopo_bond_all.h"
 
 #include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
 #include "output.h"
 #include "thermo.h"
-#include "memory.h"
+#include "update.h"
-#include "error.h"
-
 
 using namespace LAMMPS_NS;
 
@@ -58,9 +56,10 @@ void NTopoBondAll::build()
       if (atom1 == -1) {
         nmissing++;
         if (lostbond == Thermo::ERROR)
-          error->one(FLERR,"Bond atoms {} {} missing on "
+          error->one(FLERR,
-                                       "proc {} at step {}",tag[i],
+                     "Bond atoms {} {} missing on "
-                                       bond_atom[i][m],me,update->ntimestep);
+                     "proc {} at step {}",
+                     tag[i], bond_atom[i][m], me, update->ntimestep);
         continue;
       }
       atom1 = domain->closest_image(i, atom1);
@@ -81,6 +80,5 @@ void NTopoBondAll::build()
 
   int all;
   MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world);
-  if (all && (me == 0))
+  if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep);
-    error->warning(FLERR,"Bond atoms missing at step {}",update->ntimestep);
 }

src/ntopo_bond_partial.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -15,14 +14,13 @@
 #include "ntopo_bond_partial.h"
 
 #include "atom.h"
-#include "force.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
 #include "output.h"
 #include "thermo.h"
-#include "memory.h"
+#include "update.h"
-#include "error.h"
-
 
 using namespace LAMMPS_NS;
 
@@ -59,9 +57,10 @@ void NTopoBondPartial::build()
       if (atom1 == -1) {
         nmissing++;
         if (lostbond == Thermo::ERROR)
-          error->one(FLERR,"Bond atoms {} {} missing on "
+          error->one(FLERR,
-                                       "proc {} at step {}",tag[i],
+                     "Bond atoms {} {} missing on "
-                                       bond_atom[i][m],me,update->ntimestep);
+                     "proc {} at step {}",
+                     tag[i], bond_atom[i][m], me, update->ntimestep);
         continue;
       }
       atom1 = domain->closest_image(i, atom1);
@@ -82,6 +81,5 @@ void NTopoBondPartial::build()
 
   int all;
   MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world);
-  if (all && (me == 0))
+  if (all && (me == 0)) error->warning(FLERR, "Bond atoms missing at step {}", update->ntimestep);
-    error->warning(FLERR,"Bond atoms missing at step {}",update->ntimestep);
 }

src/reader.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -64,8 +63,10 @@ void Reader::open_file(const std::string &file)
 void Reader::close_file()
 {
   if (fp == nullptr) return;
-  if (compressed) platform::pclose(fp);
+  if (compressed)
-  else fclose(fp);
+    platform::pclose(fp);
+  else
+    fclose(fp);
   fp = nullptr;
 }
 
@@ -75,6 +76,5 @@ void Reader::close_file()
 
 void Reader::settings(int narg, char ** /*args*/)
 {
-  if (narg > 0)
+  if (narg > 0) error->all(FLERR, "Illegal read_dump command");
-    error->all(FLERR,"Illegal read_dump command");
 }

src/write_dump.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -61,11 +60,9 @@ void WriteDump::command(int narg, char **arg)
   // write out one frame and then delete the dump again
   // set multifile_override for DumpImage so that filename needs no "*"
 
-  if (strcmp(arg[1],"image") == 0)
+  if (strcmp(arg[1], "image") == 0) (dynamic_cast<DumpImage *>(dump))->multifile_override = 1;
-    (dynamic_cast<DumpImage *>( dump))->multifile_override = 1;
 
-  if (strcmp(arg[1],"cfg") == 0)
+  if (strcmp(arg[1], "cfg") == 0) (dynamic_cast<DumpCFG *>(dump))->multifile_override = 1;
-    (dynamic_cast<DumpCFG *>( dump))->multifile_override = 1;
 
   if ((update->first_update == 0) && (comm->me == 0))
     error->warning(FLERR, "Calling write_dump before a full system init.");