apply clang-format

src/fix_update_special_bonds.cpp

@@ -258,6 +258,6 @@ void FixUpdateSpecialBonds::write_restart(FILE *fp)
   pre_exchange();
   if (comm->me == 0) {
     int size = 0;
-    fwrite(&size,sizeof(int),1,fp);
+    fwrite(&size, sizeof(int), 1, fp);
   }
 }

src/force.cpp

@@ -346,7 +346,7 @@ Bond *Force::new_bond(const std::string &style, int trysuffix, int &sflag)
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + "/" + lmp->non_pair_suffix();
       if (bond_map->find(estyle) != bond_map->end()) {
         BondCreator &bond_creator = (*bond_map)[estyle];
@@ -414,7 +414,7 @@ Angle *Force::new_angle(const std::string &style, int trysuffix, int &sflag)
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + "/" + lmp->non_pair_suffix();
       if (angle_map->find(estyle) != angle_map->end()) {
         AngleCreator &angle_creator = (*angle_map)[estyle];
@@ -482,7 +482,7 @@ Dihedral *Force::new_dihedral(const std::string &style, int trysuffix, int &sfla
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + "/" + lmp->non_pair_suffix();
       if (dihedral_map->find(estyle) != dihedral_map->end()) {
         DihedralCreator &dihedral_creator = (*dihedral_map)[estyle];
@@ -550,7 +550,7 @@ Improper *Force::new_improper(const std::string &style, int trysuffix, int &sfla
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + "/" + lmp->non_pair_suffix();
       if (improper_map->find(estyle) != improper_map->end()) {
         ImproperCreator &improper_creator = (*improper_map)[estyle];
@@ -618,7 +618,7 @@ KSpace *Force::new_kspace(const std::string &style, int trysuffix, int &sflag)
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + "/" + lmp->non_pair_suffix();
       if (kspace_map->find(estyle) != kspace_map->end()) {
         KSpaceCreator &kspace_creator = (*kspace_map)[estyle];

src/pair_buck_coul_cut.cpp

@@ -477,8 +477,8 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype, double rsq, d
 /* ---------------------------------------------------------------------- */
 
 void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq,
-                            double factor_coul, double factor_lj, double &dupair,
+                                  double factor_coul, double factor_lj, double &dupair,
-                            double &du2pair)
+                                  double &du2pair)
 {
   double rinv, r2inv, r3inv, r6inv, r7inv, r8inv, r, rexp;
   double du_lj, du2_lj, du_coul, du2_coul;
@@ -487,7 +487,7 @@ void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq
   double qqrd2e = force->qqrd2e;
 
   r = sqrt(rsq);
-  rexp = exp(-r*rhoinv[itype][jtype]);
+  rexp = exp(-r * rhoinv[itype][jtype]);
 
   r2inv = 1.0 / rsq;
   rinv = sqrt(r2inv);

src/pair_coul_cut.cpp

@@ -331,8 +331,8 @@ double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/, double rs
 /* ---------------------------------------------------------------------- */
 
 void PairCoulCut::born_matrix(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
-                            double factor_coul, double /*factor_lj*/, double &dupair,
+                              double factor_coul, double /*factor_lj*/, double &dupair,
-                            double &du2pair)
+                              double &du2pair)
 {
   double rinv, r2inv, r3inv;
   double du_coul, du2_coul;

src/pair_lj_cut_coul_cut.cpp

@@ -462,8 +462,8 @@ double PairLJCutCoulCut::single(int i, int j, int itype, int jtype, double rsq,
 /* ---------------------------------------------------------------------- */
 
 void PairLJCutCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq,
-                            double factor_coul, double factor_lj, double &dupair,
+                                   double factor_coul, double factor_lj, double &dupair,
-                            double &du2pair)
+                                   double &du2pair)
 {
   double rinv, r2inv, r3inv, r6inv;
   double du_lj, du2_lj, du_coul, du2_coul;

src/read_data.cpp

@@ -2021,7 +2021,7 @@ void ReadData::pairIJcoeffs()
   if (eof) error->all(FLERR, "Unexpected end of data file");
 
   if (tlabelflag && !lmap->is_complete(Atom::ATOM))
-    error->all(FLERR,"Label map is incomplete: all types must be assigned a unique type label");
+    error->all(FLERR, "Label map is incomplete: all types must be assigned a unique type label");
 
   char *original = buf;
   for (i = 0; i < ntypes; i++)

src/reset_atoms_id.cpp

@@ -43,7 +43,8 @@ static int compare_coords(const int, const int, void *);
 
 /* ---------------------------------------------------------------------- */
 
-ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp) {
+ResetAtomsID::ResetAtomsID(LAMMPS *lmp) : Command(lmp)
+{
   binlo = binhi = -1;
 }
 

src/thermo.cpp

@@ -691,11 +691,12 @@ void Thermo::modify_params(int narg, char **arg)
         utils::bounds(FLERR, arg[iarg + 1], 1, nfield_initial, nlo, nhi, error);
         int icol = -1;
         for (int i = nlo - 1; i < nhi; i++) {
-          if (i < 0) icol = nfield_initial + i + 1; // doesn't happen currently
+          if (i < 0)
-          else icol = i;
+            icol = nfield_initial + i + 1;    // doesn't happen currently
+          else
+            icol = i;
           if (icol < 0 || (icol >= nfield_initial))
-            error->all(FLERR, "Invalid thermo_modify format argument: {}",
+            error->all(FLERR, "Invalid thermo_modify format argument: {}", arg[iarg + 1]);
-              arg[iarg + 1]);
           format_column_user[icol] = arg[iarg + 2];
         }
       } else {
@@ -1135,7 +1136,8 @@ void Thermo::check_temp(const std::string &keyword)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init temperature",
                keyword);
   if (!temperature->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
+    error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
+               keyword);
   if (!(temperature->invoked_flag & Compute::INVOKED_SCALAR)) {
     temperature->compute_scalar();
     temperature->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1154,7 +1156,8 @@ void Thermo::check_pe(const std::string &keyword)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init potential energy",
                keyword);
   if (!pe->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
+    error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
+               keyword);
   if (!(pe->invoked_flag & Compute::INVOKED_SCALAR)) {
     pe->compute_scalar();
     pe->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1170,7 +1173,8 @@ void Thermo::check_press_scalar(const std::string &keyword)
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
   if (!pressure->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
+    error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
+               keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_SCALAR)) {
     pressure->compute_scalar();
     pressure->invoked_flag |= Compute::INVOKED_SCALAR;
@@ -1186,7 +1190,8 @@ void Thermo::check_press_vector(const std::string &keyword)
   if (!pressure)
     error->all(FLERR, "Thermo keyword {} in variable requires thermo to use/init press", keyword);
   if (!pressure->is_initialized())
-    error->all(FLERR,"Thermo keyword {} cannot be invoked before initialization by a run",keyword);
+    error->all(FLERR, "Thermo keyword {} cannot be invoked before initialization by a run",
+               keyword);
   if (!(pressure->invoked_flag & Compute::INVOKED_VECTOR)) {
     pressure->compute_vector();
     pressure->invoked_flag |= Compute::INVOKED_VECTOR;

src/update.cpp

@@ -362,7 +362,7 @@ void Update::new_integrate(char *style, int narg, char **arg, int trysuffix, int
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + std::string("/") + lmp->non_pair_suffix();
       if (integrate_map->find(estyle) != integrate_map->end()) {
         IntegrateCreator &integrate_creator = (*integrate_map)[estyle];
@@ -428,7 +428,7 @@ void Update::new_minimize(char *style, int /* narg */, char ** /* arg */, int tr
 {
   if (trysuffix && lmp->suffix_enable) {
     if (lmp->non_pair_suffix()) {
-      sflag = 1 + 2*lmp->pair_only_flag;
+      sflag = 1 + 2 * lmp->pair_only_flag;
       std::string estyle = style + std::string("/") + lmp->non_pair_suffix();
       if (minimize_map->find(estyle) != minimize_map->end()) {
         MinimizeCreator &minimize_creator = (*minimize_map)[estyle];