apply clang-format

src/BPM/bond_bpm.cpp

@@ -319,8 +319,7 @@ void BondBPM::write_restart(FILE *fp)
 
 void BondBPM::read_restart(FILE *fp)
 {
-  if (comm->me == 0)
+  if (comm->me == 0) utils::sfread(FLERR, &overlay_flag, sizeof(int), 1, fp, nullptr, error);
-    utils::sfread(FLERR, &overlay_flag, sizeof(int), 1, fp, nullptr, error);
   MPI_Bcast(&overlay_flag, 1, MPI_INT, 0, world);
 }
 

src/BPM/bond_bpm_rotational.h

@@ -43,8 +43,8 @@ class BondBPMRotational : public BondBPM {
   double *Fcr, *Fcs, *Tct, *Tcb;
   int smooth_flag;
 
-  double elastic_forces(int, int, int, double, double, double, double *, double *,
+  double elastic_forces(int, int, int, double, double, double, double *, double *, double *,
-                        double *, double *, double *, double *);
+                        double *, double *, double *);
   void damping_forces(int, int, int, double *, double *, double *, double *, double *);
 
   void allocate();

src/BPM/bond_bpm_spring.cpp

@@ -356,8 +356,7 @@ void BondBPMSpring::write_restart_settings(FILE *fp)
 
 void BondBPMSpring::read_restart_settings(FILE *fp)
 {
-  if (comm->me == 0)
+  if (comm->me == 0) utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error);
-    utils::sfread(FLERR, &smooth_flag, sizeof(int), 1, fp, nullptr, error);
   MPI_Bcast(&smooth_flag, 1, MPI_INT, 0, world);
 }
 

src/ELECTRODE/slab_dipole.cpp

@@ -37,13 +37,13 @@ using namespace MathConst;
 */
 SlabDipole::SlabDipole(LAMMPS *lmp) : BoundaryCorrection(lmp){};
 
-void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom,
+void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom, int eflag_global,
-                              int eflag_global, double &energy, double *eatom)
+                              double &energy, double *eatom)
 {
   // compute local contribution to global dipole moment
   double *q = atom->q;
   double **x = atom->x;
-  double zprd_slab = domain->zprd*slab_volfactor;
+  double zprd_slab = domain->zprd * slab_volfactor;
   int nlocal = atom->nlocal;
   double dipole = 0.0;
   for (int i = 0; i < nlocal; i++) dipole += q[i] * x[i][2];
@@ -65,7 +65,8 @@ void SlabDipole::compute_corr(double qsum, double slab_volfactor, int eflag_atom
 
   // compute corrections
   double const e_slabcorr = MY_2PI *
-      (dipole_all * dipole_all - qsum * dipole_r2 - qsum * qsum * zprd_slab * zprd_slab / 12.0) / volume;
+      (dipole_all * dipole_all - qsum * dipole_r2 - qsum * qsum * zprd_slab * zprd_slab / 12.0) /
+      volume;
   double const qscale = qqrd2e * scale;
   if (eflag_global) energy += qscale * e_slabcorr;
 

src/INTEL/pair_buck_coul_cut_intel.h

@@ -15,7 +15,6 @@
    Contributing author: Rodrigo Canales (RWTH Aachen University)
 ------------------------------------------------------------------------- */
 
-
 #ifdef PAIR_CLASS
 // clang-format off
 PairStyle(buck/coul/cut/intel,PairBuckCoulCutIntel);

src/LATTE/fix_latte.h

@@ -47,7 +47,7 @@ class FixLatte : public Fix {
   int coulomb, pbcflag, pe_peratom, virial_global, virial_peratom, neighflag;
   int exclude, excludebit;
   int eflag_caller;
-  char *id_pe,*id_exclude;
+  char *id_pe, *id_exclude;
   int *exclusion_group_ptr;
   int setupflag, newsystem;
   bigint natoms_last;

src/MISC/pair_list.cpp

@@ -172,7 +172,8 @@ void PairList::compute(int eflag, int vflag)
         const double dexp = exp(-par.param.morse.alpha * dr);
         fpair = 2.0 * par.param.morse.d0 * par.param.morse.alpha * (dexp * dexp - dexp) / r;
 
-        if (eflag_either) epair = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp + 1.0) - par.offset;
+        if (eflag_either)
+          epair = par.param.morse.d0 * (dexp * dexp - 2.0 * dexp + 1.0) - par.offset;
 
       } else if (par.style == LJ126) {
 

src/MISC/pair_list.h

@@ -53,7 +53,6 @@ class PairList : public Pair {
     double k, b1, b2;
   };
 
-
   union param_u {
     harm_p harm;
     morse_p morse;

src/ML-PACE/pair_pace_extrapolation.cpp

@@ -382,10 +382,10 @@ void PairPACEExtrapolation::coeff(int narg, char **arg)
   aceimpl->ace->load_active_set(active_set_inv_filename);
   bool is_linear_extrapolation_grade = aceimpl->ace->get_is_linear_extrapolation_grade();
   if (comm->me == 0) {
-        if (is_linear_extrapolation_grade)
+    if (is_linear_extrapolation_grade)
-            utils::logmesg(lmp, "LINEAR ASI is loaded\n");
+      utils::logmesg(lmp, "LINEAR ASI is loaded\n");
-        else
+    else
-            utils::logmesg(lmp, "FULL ASI is loaded\n");
+      utils::logmesg(lmp, "FULL ASI is loaded\n");
   }
 
   // clear setflag since coeff() called once with I,J = * *

src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.h

@@ -32,8 +32,7 @@ class PairLJCutCoulCutDielectricOMP : public PairLJCutCoulCutDielectric, public
   void compute(int, int) override;
 
  protected:
-  template <int EVFLAG, int EFLAG>
+  template <int EVFLAG, int EFLAG> void eval(int ifrom, int ito, ThrData *const thr);
-  void eval(int ifrom, int ito, ThrData *const thr);
 };
 
 }    // namespace LAMMPS_NS

src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.h

@@ -32,8 +32,7 @@ class PairLJCutCoulDebyeDielectricOMP : public PairLJCutCoulDebyeDielectric, pub
   void compute(int, int) override;
 
  protected:
-  template <int EVFLAG, int EFLAG>
+  template <int EVFLAG, int EFLAG> void eval(int ifrom, int ito, ThrData *const thr);
-  void eval(int ifrom, int ito, ThrData *const thr);
 };
 
 }    // namespace LAMMPS_NS

src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.h

@@ -33,8 +33,7 @@ class PairLJCutCoulLongDielectricOMP : public PairLJCutCoulLongDielectric, publi
   void compute(int, int) override;
 
  protected:
-  template <int EVFLAG, int EFLAG>
+  template <int EVFLAG, int EFLAG> void eval(int ifrom, int ito, ThrData *const thr);
-  void eval(int ifrom, int ito, ThrData *const thr);
 };
 
 }    // namespace LAMMPS_NS

src/bond.cpp

@@ -255,11 +255,10 @@ void Bond::ev_tally(int i, int j, int nlocal, int newton_bond, double ebond, dou
    for virial, have delx,dely,delz and fx,fy,fz
 ------------------------------------------------------------------------- */
 
-void Bond::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
+void Bond::ev_tally_xyz(int i, int j, int nlocal, int newton_bond, double ebond, double fx,
-                        double ebond, double fx, double fy, double fz,
+                        double fy, double fz, double delx, double dely, double delz)
-                        double delx, double dely, double delz)
 {
-  double ebondhalf,v[6];
+  double ebondhalf, v[6];
 
   if (eflag_either) {
     if (eflag_global) {

src/bond_hybrid.cpp

@@ -257,10 +257,9 @@ void BondHybrid::flags()
   // set comm_forward, comm_reverse, comm_reverse_off to max of any sub-style
 
   for (m = 0; m < nstyles; m++) {
-    if (styles[m]) comm_forward = MAX(comm_forward,styles[m]->comm_forward);
+    if (styles[m]) comm_forward = MAX(comm_forward, styles[m]->comm_forward);
-    if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
+    if (styles[m]) comm_reverse = MAX(comm_reverse, styles[m]->comm_reverse);
-    if (styles[m]) comm_reverse_off = MAX(comm_reverse_off,
+    if (styles[m]) comm_reverse_off = MAX(comm_reverse_off, styles[m]->comm_reverse_off);
-                                          styles[m]->comm_reverse_off);
   }
 
   init_svector();
@@ -276,8 +275,7 @@ void BondHybrid::init_svector()
   // allocate svector
 
   single_extra = 0;
-  for (int m = 0; m < nstyles; m++)
+  for (int m = 0; m < nstyles; m++) single_extra = MAX(single_extra, styles[m]->single_extra);
-    single_extra = MAX(single_extra,styles[m]->single_extra);
 
   if (single_extra) {
     delete[] svector;
@@ -415,14 +413,12 @@ double BondHybrid::single(int type, double rsq, int i, int j, double &fforce)
 
 void BondHybrid::copy_svector(int type)
 {
-  memset(svector,0,single_extra*sizeof(double));
+  memset(svector, 0, single_extra * sizeof(double));
 
   // there is only one style in bond style hybrid for a bond type
   Bond *this_style = styles[map[type]];
 
-  for (int l = 0; this_style->single_extra; ++l) {
+  for (int l = 0; this_style->single_extra; ++l) { svector[l] = this_style->svector[l]; }
-    svector[l] = this_style->svector[l];
-  }
 }
 
 /* ----------------------------------------------------------------------

src/dump.h

@@ -45,9 +45,15 @@ class Dump : protected Pointers {
   void init();
   virtual void write();
 
-  virtual int pack_forward_comm(int, int *, double *, int, int *) { return 0; }
+  virtual int pack_forward_comm(int, int *, double *, int, int *)
+  {
+    return 0;
+  }
   virtual void unpack_forward_comm(int, int, double *) {}
-  virtual int pack_reverse_comm(int, int, double *) { return 0; }
+  virtual int pack_reverse_comm(int, int, double *)
+  {
+    return 0;
+  }
   virtual void unpack_reverse_comm(int, int *, double *) {}
 
   void modify_params(int, char **);
@@ -91,9 +97,9 @@ class Dump : protected Pointers {
   char *refresh;      // compute ID to invoke refresh() on
   int irefresh;       // index of compute
 
-  int skipflag;       // 1 if skip condition defined
+  int skipflag;     // 1 if skip condition defined
-  char *skipvar;      // name of variable to check for skip condition
+  char *skipvar;    // name of variable to check for skip condition
-  int skipindex;      // index of skip variable
+  int skipindex;    // index of skip variable
 
   char boundstr[9];    // encoding of boundary flags
 
@@ -151,11 +157,17 @@ class Dump : protected Pointers {
 
   virtual void init_style() = 0;
   virtual void openfile();
-  virtual int modify_param(int, char **) { return 0; }
+  virtual int modify_param(int, char **)
+  {
+    return 0;
+  }
   virtual void write_header(bigint) = 0;
   virtual int count();
   virtual void pack(tagint *) = 0;
-  virtual int convert_string(int, double *) { return 0; }
+  virtual int convert_string(int, double *)
+  {
+    return 0;
+  }
   virtual void write_data(int, double *) = 0;
   virtual void write_footer() {}
 

src/fix_bond_history.cpp

@@ -87,8 +87,8 @@ void FixBondHistory::post_constructor()
 
   id_fix = utils::strdup(id + std::string("_FIX_PROP_ATOM"));
   id_array = utils::strdup(std::string("d2_") + id);
-  modify->add_fix(fmt::format("{} {} property/atom {} {} writedata no", id_fix, group->names[igroup], id_array,
+  modify->add_fix(fmt::format("{} {} property/atom {} {} writedata no", id_fix,
-                              nbond * ndata));
+                              group->names[igroup], id_array, nbond * ndata));
   int tmp1, tmp2;
   index = atom->find_custom(&id_array[3], tmp1, tmp2);
 }

src/fix_pair.h

@@ -46,10 +46,10 @@ class FixPair : public Fix {
   double memory_usage() override;
 
  private:
-  int nevery,nfield,ncols;
+  int nevery, nfield, ncols;
   bigint lasttime;
   char *pairname;
-  char **fieldname,**triggername;
+  char **fieldname, **triggername;
   int *trigger;
   int **triggerptr;
 

src/fix_property_atom.cpp

@@ -154,8 +154,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
       border = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
     } else if (strcmp(arg[iarg], "writedata") == 0) {
-      if (iarg+2 > narg) error->all(FLERR,"Illegal fix property/atom command");
+      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command");
-      wd_section = utils::logical(FLERR,arg[iarg+1],false,lmp);
+      wd_section = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       iarg += 2;
     } else
       error->all(FLERR, "Illegal fix property/atom command");

src/fix_update_special_bonds.cpp

@@ -54,7 +54,7 @@ void FixUpdateSpecialBonds::setup(int /*vflag*/)
   // error if more than one fix update/special/bonds
 
   if (modify->get_fix_by_style("UPDATE_SPECIAL_BONDS").size() > 1)
-    error->all(FLERR,"More than one fix update/special/bonds");
+    error->all(FLERR, "More than one fix update/special/bonds");
 
   // Require atoms know about all of their bonds and if they break
   if (force->newton_bond) error->all(FLERR, "Fix update/special/bonds requires Newton bond off");
@@ -131,14 +131,14 @@ void FixUpdateSpecialBonds::pre_exchange()
     // ignore n2, n3 since 1-3, 1-4 special factors required to be 1.0
     n1 = nspecial[i][0];
     if (n1 >= atom->maxspecial)
-      error->one(FLERR,"Special list size exceeded in fix update/special/bond");
+      error->one(FLERR, "Special list size exceeded in fix update/special/bond");
     special[i][n1] = tagj;
     nspecial[i][0] += 1;
     nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
 
     n1 = nspecial[j][0];
     if (n1 >= atom->maxspecial)
-      error->one(FLERR,"Special list size exceeded in fix update/special/bond");
+      error->one(FLERR, "Special list size exceeded in fix update/special/bond");
     special[j][n1] = tagi;
     nspecial[j][0] += 1;
     nspecial[j][1] = nspecial[j][2] = nspecial[j][0];
@@ -210,8 +210,8 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
       jnum = numneigh[i1];
       for (jj = 0; jj < jnum; jj++) {
         j = jlist[jj];
-        if (((j >> SBBITS) & 3) != 0) continue;              // Skip bonded pairs
+        if (((j >> SBBITS) & 3) != 0) continue;               // Skip bonded pairs
-        if (tag[j] == tag2) jlist[jj] = j ^ (1 << SBBITS);   // Add 1-2 special bond bits
+        if (tag[j] == tag2) jlist[jj] = j ^ (1 << SBBITS);    // Add 1-2 special bond bits
       }
     }
 
@@ -220,8 +220,8 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/)
       jnum = numneigh[i2];
       for (jj = 0; jj < jnum; jj++) {
         j = jlist[jj];
-        if (((j >> SBBITS) & 3) != 0) continue;              // Skip bonded pairs
+        if (((j >> SBBITS) & 3) != 0) continue;               // Skip bonded pairs
-        if (tag[j] == tag1) jlist[jj] = j ^ (1 << SBBITS);   // Add 1-2 special bond bits
+        if (tag[j] == tag1) jlist[jj] = j ^ (1 << SBBITS);    // Add 1-2 special bond bits
       }
     }
   }

src/fix_vector.cpp

@@ -47,8 +47,7 @@ FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
     val.id = argi.get_name();
     val.val.c = nullptr;
 
-    if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) ||
+    if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1))
-        (argi.get_dim() > 1))
       error->all(FLERR, "Invalid fix vector argument: {}", arg[iarg]);
 
     values.push_back(val);

src/library.cpp

@@ -3020,10 +3020,11 @@ Below is a brief C code demonstrating accessing this collected bond information.
 
 .. code-block:: c
 
+   #include "library.h"
+
+   #include <stdint.h>
    #include <stdio.h>
    #include <stdlib.h>
-   #include <stdint.h>
-   #include "library.h"
 
    int main(int argc, char **argv)
    {

src/memory.h

@@ -1,3 +1,4 @@
+// clang-format off
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -647,16 +648,15 @@ class Memory : protected Pointers {
 ------------------------------------------------------------------------- */
 
   template <typename TYPE>
-  TYPE ****create4d_offset_last(TYPE ****&array, int n1lo, int n1hi,
+  TYPE ****create4d_offset_last(TYPE ****&array, int n1lo, int n1hi, int n2lo, int n2hi, int n3lo,
-                                int n2lo, int n2hi, int n3lo, int n3hi, int n4,
+                                int n3hi, int n4, const char *name)
-                                const char *name)
   {
     if (n1lo > n1hi || n2lo > n2hi || n3lo > n3hi || n4 <= 0) return nullptr;
 
     int n1 = n1hi - n1lo + 1;
     int n2 = n2hi - n2lo + 1;
     int n3 = n3hi - n3lo + 1;
-    create(array,n1,n2,n3,n4,name);
+    create(array, n1, n2, n3, n4, name);
 
     bigint m = ((bigint) n1) * n2;
     for (bigint i = 0; i < m; i++) array[0][i] -= n3lo;
@@ -666,19 +666,20 @@ class Memory : protected Pointers {
   }
 
   template <typename TYPE>
-  TYPE ****create4d_offset_last(TYPE *****& /*array*/, int /*n1lo*/, int /*n1hi*/,
+  TYPE ****create4d_offset_last(TYPE *****& /*array*/, int /*n1lo*/, int /*n1hi*/, int /*n2lo*/,
-                                int /*n2lo*/, int /*n2hi*/,
+                                int /*n2hi*/, int /*n3lo*/, int /*n3hi*/, int /*n4*/,
-                                int /*n3lo*/, int /*n3hi*/, int /*n4*/,
                                 const char *name)
-  {fail(name); return nullptr;}
+  {
+    fail(name);
+    return nullptr;
+  }
 
 /* ----------------------------------------------------------------------
    free a 4d array with indices 1,2,3 offset
 ------------------------------------------------------------------------- */
 
   template <typename TYPE>
-  void destroy4d_offset_last(TYPE ****&array,
+  void destroy4d_offset_last(TYPE ****&array, int n1_offset, int n2_offset, int n3_offset)
-                             int n1_offset, int n2_offset, int n3_offset)
   {
     if (array == nullptr) return;
     sfree(&array[n1_offset][n2_offset][n3_offset][0]);

src/modify.cpp

@@ -806,10 +806,12 @@ Fix *Modify::add_fix(int narg, char **arg, int trysuffix)
   //   since some fixes access domain settings in their constructor
   // nullptr must be last entry in this list
 
+  // clang-format off
   const char *exceptions[] =
     {"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx",
      "deprecated", "STORE/KIM", "amoeba/pitorsion", "amoeba/bitorsion",
      nullptr};
+  // clang-format on
 
   if (domain->box_exist == 0) {
     int m;