auto loop optimizations

src/MISC/fix_srp.cpp

@@ -118,11 +118,10 @@ void FixSRP::init()
   // because this fix's pre_exchange() creates per-atom data structure
   // that data must be current for atom migration to carry it along
 
-  for (int i = 0; i < modify->nfix; i++) {
-    if (modify->fix[i] == this) break;
-    if (modify->fix[i]->pre_exchange_migrate)
-      error->all(FLERR,"Fix SRP comes after a fix which "
-                 "migrates atoms in pre_exchange");
+  for (auto &ifix : modify->get_fix_list()) {
+    if (ifix == this) break;
+    if (ifix->pre_exchange_migrate)
+      error->all(FLERR,"Fix {} comes after a fix which migrates atoms in pre_exchange", style);
   }
 
   // setup neigh exclusions for diff atom types

src/PLUGIN/plugin.cpp

@@ -369,7 +369,7 @@ void plugin_unload(const char *style, const char *name, LAMMPS *lmp)
 
     // must delete all compute instances using this compute style
 
-    for (auto icompute : lmp->modify->get_compute_by_style(name))
+    for (auto &icompute : lmp->modify->get_compute_by_style(name))
       lmp->modify->delete_compute(icompute->id);
 
   } else if (pstyle == "fix") {
@@ -380,7 +380,7 @@ void plugin_unload(const char *style, const char *name, LAMMPS *lmp)
 
     // must delete all fix instances using this fix style
 
-    for (auto ifix : lmp->modify->get_fix_by_style(name)) lmp->modify->delete_fix(ifix->id);
+    for (auto &ifix : lmp->modify->get_fix_by_style(name)) lmp->modify->delete_fix(ifix->id);
 
   } else if (pstyle == "region") {
 
@@ -388,7 +388,7 @@ void plugin_unload(const char *style, const char *name, LAMMPS *lmp)
     auto found = region_map->find(name);
     if (found != region_map->end()) region_map->erase(name);
 
-    for (auto iregion : lmp->domain->get_region_by_style(name)) lmp->domain->delete_region(iregion);
+    for (auto &iregion : lmp->domain->get_region_by_style(name)) lmp->domain->delete_region(iregion);
 
   } else if (pstyle == "command") {
 

src/POEMS/fix_poems.cpp

@@ -353,7 +353,7 @@ void FixPOEMS::init()
 
   if (earlyflag) {
     bool pflag = false;
-    for (auto ifix : modify->get_fix_list()) {
+    for (auto &ifix : modify->get_fix_list()) {
       if (utils::strmatch(ifix->style, "^poems")) pflag = true;
       if (pflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
         if (comm->me == 0)
@@ -364,7 +364,7 @@ void FixPOEMS::init()
 
   // error if npt,nph fix comes before rigid fix
   bool pflag = false;
-  for (auto ifix : modify->get_fix_list()) {
+  for (auto &ifix : modify->get_fix_list()) {
     if (!pflag && utils::strmatch(ifix->style, "np[th]"))
       error->all(FLERR, "POEMS fix must come before NPT/NPH fix");
     if (utils::strmatch(ifix->style, "^poems")) pflag = true;

src/REPLICA/hyper.cpp

@@ -155,10 +155,10 @@ void Hyper::command(int narg, char **arg)
 
   // cannot use hyper with time-dependent fixes or regions
 
-  for (auto ifix : modify->get_fix_list())
+  for (auto &ifix : modify->get_fix_list())
     if (ifix->time_depend) error->all(FLERR,"Cannot use hyper with a time-dependent fix defined");
 
-  for (auto reg : domain->get_region_list())
+  for (auto &reg : domain->get_region_list())
     if (reg->dynamic_check())
       error->all(FLERR,"Cannot use hyper with a time-dependent region defined");
 
@@ -180,9 +180,7 @@ void Hyper::command(int narg, char **arg)
 
   fix_event->store_state_quench();
   quench(1);
-  if (dumpflag)
-    for (int idump = 0; idump < ndump; idump++)
-      output->dump[dumplist[idump]]->write();
+  if (dumpflag) for (auto &idump : dumplist) idump->write();
   fix_event->store_event();
   if (hyperenable) fix_hyper->build_bond_list(0);
   fix_event->restore_state_quench();
@@ -211,9 +209,7 @@ void Hyper::command(int narg, char **arg)
       nevent++;
       nevent_atoms += ecount;
 
-      if (dumpflag)
-        for (int idump = 0; idump < ndump; idump++)
-          output->dump[dumplist[idump]]->write();
+      if (dumpflag) for (auto &idump : dumplist) idump->write();
       fix_event->store_event();
       if (hyperenable) fix_hyper->build_bond_list(ecount);
 

src/REPLICA/prd.cpp

@@ -229,10 +229,10 @@ void PRD::command(int narg, char **arg)
 
   // cannot use PRD with time-dependent fixes or regions
 
-  for (auto ifix : modify->get_fix_list())
+  for (auto &ifix : modify->get_fix_list())
     if (ifix->time_depend) error->all(FLERR,"Cannot use PRD with a time-dependent fix defined");
 
-  for (auto reg : domain->get_region_list())
+  for (auto &reg : domain->get_region_list())
     if (reg->dynamic_check())
       error->all(FLERR,"Cannot use PRD with a time-dependent region defined");
 

src/RIGID/fix_rigid.cpp

@@ -684,13 +684,13 @@ void FixRigid::init()
   // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
-  for (auto ifix : modify->get_fix_list())
+  for (auto &ifix : modify->get_fix_list())
     if (ifix->rigid_flag) count++;
   if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
 
   if (earlyflag) {
     bool rflag = false;
-    for (auto ifix : modify->get_fix_list()) {
+    for (auto &ifix : modify->get_fix_list()) {
       if (ifix->rigid_flag) rflag = true;
       if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
         error->warning(FLERR,"Fix {} with ID {} alters forces after fix rigid",
@@ -713,7 +713,7 @@ void FixRigid::init()
   //  error if a fix changing the box comes before rigid fix
 
   bool boxflag = false;
-  for (auto ifix : modify->get_fix_list()) {
+  for (auto &ifix : modify->get_fix_list()) {
     if (boxflag && utils::strmatch(ifix->style,"^rigid"))
         error->all(FLERR,"Rigid fixes must come before any box changing fix");
     if (ifix->box_change) boxflag = true;

src/RIGID/fix_rigid_small.cpp

@@ -529,13 +529,13 @@ void FixRigidSmall::init()
   // if earlyflag, warn if any post-force fixes come after a rigid fix
 
   int count = 0;
-  for (auto ifix : modify->get_fix_list())
+  for (auto &ifix : modify->get_fix_list())
     if (ifix->rigid_flag) count++;
   if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
 
   if (earlyflag) {
     bool rflag = false;
-    for (auto ifix : modify->get_fix_list()) {
+    for (auto &ifix : modify->get_fix_list()) {
       if (ifix->rigid_flag) rflag = true;
       if ((comm->me == 0) && rflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag)
         error->warning(FLERR,"Fix {} with ID {} alters forces after fix rigid/small",
@@ -558,7 +558,7 @@ void FixRigidSmall::init()
   // error if a fix changing the box comes before rigid fix
 
   bool boxflag = false;
-  for (auto ifix : modify->get_fix_list()) {
+  for (auto &ifix : modify->get_fix_list()) {
     if (boxflag && utils::strmatch(ifix->style,"^rigid"))
         error->all(FLERR,"Rigid fixes must come before any box changing fix");
     if (ifix->box_change) boxflag = true;

src/RIGID/fix_shake.cpp

@@ -347,16 +347,12 @@ void FixShake::init()
   if (update->whichflag == 2)
     error->all(FLERR,"Fix shake cannot be used with minimization");
 
-  // error if npt,nph fix comes before shake fix
-
-  for (i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"npt") == 0) break;
-    if (strcmp(modify->fix[i]->style,"nph") == 0) break;
-  }
-  if (i < modify->nfix) {
-    for (int j = i; j < modify->nfix; j++)
-      if (strcmp(modify->fix[j]->style,"shake") == 0)
-        error->all(FLERR,"Shake fix must come before NPT/NPH fix");
+  // error if a fix changing the box comes before shake fix
+  bool boxflag = false;
+  for (auto &ifix : modify->get_fix_list()) {
+   if (boxflag && utils::strmatch(ifix->style,pattern))
+     error->all(FLERR,"Fix {} must come before any box changing fix", style);
+    if (ifix->box_change) boxflag = true;
   }
 
   // if rRESPA, find associated fix that must exist

src/domain.cpp

@@ -125,7 +125,7 @@ Domain::~Domain()
 {
   if (copymode) return;
 
-  for (auto reg : regions) delete reg;
+  for (auto &reg : regions) delete reg;
   regions.clear();
   delete lattice;
   delete region_map;
@@ -190,7 +190,7 @@ void Domain::init()
 
   // region inits
 
-  for (auto reg : regions) reg->init();
+  for (auto &reg : regions) reg->init();
 }
 
 /* ----------------------------------------------------------------------

src/fix_deform.cpp

@@ -882,7 +882,7 @@ void FixDeform::end_of_step()
       if (mask[i] & groupbit)
         domain->x2lamda(x[i],x[i]);
 
-    for (auto ifix : rfix)
+    for (auto &ifix : rfix)
       ifix->deform(0);
   }
 
@@ -921,7 +921,7 @@ void FixDeform::end_of_step()
       if (mask[i] & groupbit)
         domain->lamda2x(x[i],x[i]);
 
-    for (auto ifix : rfix)
+    for (auto &ifix : rfix)
       ifix->deform(1);
   }
 

src/utils.cpp

@@ -1087,7 +1087,7 @@ bool utils::is_integer(const std::string &str)
 {
   if (str.empty()) return false;
 
-  for (auto c : str) {
+  for (const auto &c : str) {
     if (isdigit(c) || c == '-' || c == '+') continue;
     return false;
   }
@@ -1102,7 +1102,7 @@ bool utils::is_double(const std::string &str)
 {
   if (str.empty()) return false;
 
-  for (auto c : str) {
+  for (const auto &c : str) {
     if (isdigit(c)) continue;
     if (c == '-' || c == '+' || c == '.') continue;
     if (c == 'e' || c == 'E') continue;
@@ -1119,7 +1119,7 @@ bool utils::is_id(const std::string &str)
 {
   if (str.empty()) return false;
 
-  for (auto c : str) {
+  for (const auto &c : str) {
     if (isalnum(c) || (c == '_')) continue;
     return false;
   }