simplify by using utils::strdup() fmt::format() and reorder includes

src/USER-BOCS/fix_bocs.cpp

@@ -1525,9 +1525,7 @@ int FixBocs::modify_param(int narg, char **arg)
       tcomputeflag = 0;
     }
     delete [] id_temp;
-    int n = strlen(arg[1]) + 1;
+    id_temp = utils::strdup(arg[1]);
-    id_temp = new char[n];
-    strcpy(id_temp,arg[1]);
 
     int icompute = modify->find_compute(arg[1]);
     if (icompute < 0)
@@ -1559,9 +1557,7 @@ int FixBocs::modify_param(int narg, char **arg)
       pcomputeflag = 0;
     }
     delete [] id_press;
-    int n = strlen(arg[1]) + 1;
+    id_press = utils::strdup(arg[1]);
-    id_press = new char[n];
-    strcpy(id_press,arg[1]);
 
     int icompute = modify->find_compute(arg[1]);
     if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");

src/USER-DPD/fix_eos_table_rx.cpp

@@ -17,16 +17,15 @@
 
 #include "fix_eos_table_rx.h"
 
-
-#include <cstring>
-#include <cmath>
 #include "atom.h"
+#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "comm.h"
 #include "modify.h"
 
+#include <cmath>
+#include <cstring>
 
 #define MAXLINE 1024
 

src/USER-DPD/fix_rx.cpp

@@ -13,28 +13,26 @@
 
 #include "fix_rx.h"
 
-
-#include <cstring>
-#include <cmath>
-#include <cfloat> // DBL_EPSILON
 #include "atom.h"
-#include "error.h"
-#include "group.h"
-#include "modify.h"
-#include "force.h"
-#include "memory.h"
 #include "comm.h"
-#include "update.h"
 #include "domain.h"
-#include "neighbor.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
+#include "math_special.h"
+#include "memory.h"
+#include "modify.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "math_special.h"
+#include "neighbor.h"
 #include "pair_dpd_fdt_energy.h"
+#include "update.h"
 
-
-#include <vector> // std::vector<>
 #include <algorithm> // std::max
+#include <cfloat> // DBL_EPSILON
+#include <cmath>
+#include <cstring>
+#include <vector> // std::vector<>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/USER-DPD/pair_exp6_rx.cpp

@@ -13,20 +13,19 @@
 
 #include "pair_exp6_rx.h"
 
-#include <cmath>
-
-#include <cstring>
-#include <cfloat>
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
+#include "fix.h"
 #include "force.h"
-#include "neigh_list.h"
 #include "math_special.h"
 #include "memory.h"
-#include "error.h"
-
 #include "modify.h"
-#include "fix.h"
+#include "neigh_list.h"
+
+#include <cfloat>
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;

src/USER-DPD/pair_multi_lucy.cpp

@@ -21,21 +21,19 @@
    The Journal of Chemical Physics, 2016, 144, 104501.
 ------------------------------------------------------------------------------------------- */
 
+#include "pair_multi_lucy.h"
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "math_const.h"
+#include "memory.h"
+#include "neigh_list.h"
 
 #include <cmath>
-#include "math_const.h"
-
 #include <cstring>
-#include "pair_multi_lucy.h"
-#include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-#include "citeme.h"
-
 
 using namespace LAMMPS_NS;
 

src/USER-DPD/pair_multi_lucy_rx.cpp

@@ -21,23 +21,21 @@
    The Journal of Chemical Physics, 2016, 144, 104501.
 ------------------------------------------------------------------------------------------- */
 
+#include "pair_multi_lucy_rx.h"
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "fix.h"
+#include "force.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
 
 #include <cmath>
-#include "math_const.h"
-
 #include <cstring>
-#include "pair_multi_lucy_rx.h"
-#include "atom.h"
-#include "force.h"
-#include "comm.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-
-#include "citeme.h"
-#include "modify.h"
-#include "fix.h"
-
 
 using namespace LAMMPS_NS;
 

src/USER-EFF/fix_temp_rescale_eff.cpp

@@ -165,9 +165,7 @@ int FixTempRescaleEff::modify_param(int narg, char **arg)
       tflag = 0;
     }
     delete [] id_temp;
-    int n = strlen(arg[1]) + 1;
+    id_temp = utils::strdup(arg[1]);
-    id_temp = new char[n];
-    strcpy(id_temp,arg[1]);
 
     int icompute = modify->find_compute(id_temp);
     if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");

src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp

@@ -31,10 +31,8 @@
 
 ------------------------------------------------------------------------- */
 
-
 #include "fix_nve_manifold_rattle.h"
 
-#include <cstring>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
@@ -44,18 +42,17 @@
 #include "citeme.h"
 #include "comm.h"
 
+#include <cstring>
+
 #include "manifold_factory.h"
 #include "manifold.h"
 
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace user_manifold;
 
-
 enum { CONST, EQUAL }; // For treating the variables.
 
-
 static const char* cite_fix_nve_manifold_rattle =
   "fix nve/manifold/rattle command:\n\n"
   "@article{paquay-2016,\n"

src/USER-MGPT/pair_mgpt.cpp

@@ -23,20 +23,18 @@
 
 #include "pair_mgpt.h"
 
-#include <cmath>
-
-#include <cstring>
-#include <cassert>
-
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "memory.h"
+#include "neighbor.h"
-#include "error.h"
 
+#include <cassert>
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/USER-MISC/compute_gyration_shape.cpp

@@ -15,17 +15,18 @@
  *    Contributing author:  Evangelos Voyiatzis (Royal DSM)
  * ------------------------------------------------------------------------- */
 
-
 #include "compute_gyration_shape.h"
-#include <cmath>
+
-#include <cstring>
 #include "error.h"
-#include "math_extra.h"
 #include "math_eigen.h"
+#include "math_extra.h"
 #include "math_special.h"
 #include "modify.h"
 #include "update.h"
 
+#include <cmath>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
@@ -41,9 +42,7 @@ ComputeGyrationShape::ComputeGyrationShape(LAMMPS *lmp, int narg, char **arg) :
   extvector = 0;
 
   // ID of compute gyration
-  int n = strlen(arg[3]) + 1;
+  id_gyration = utils::strdup(arg[3]);
-  id_gyration = new char[n];
-  strcpy(id_gyration,arg[3]);
 
   init();
 

src/USER-MISC/compute_gyration_shape_chunk.cpp

@@ -15,17 +15,18 @@
  *    Contributing author:  Evangelos Voyiatzis (Royal DSM)
  * ------------------------------------------------------------------------- */
 
-
 #include "compute_gyration_shape_chunk.h"
+
+#include "error.h"
+#include "math_eigen.h"
+#include "math_extra.h"
+#include "math_special.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
 #include <cmath>
 #include <cstring>
-#include "error.h"
-#include "math_extra.h"
-#include "math_eigen.h"
-#include "math_special.h"
-#include "modify.h"
-#include "memory.h"
-#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -37,9 +38,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char
   if (narg != 4) error->all(FLERR,"Illegal compute gyration/shape/chunk command");
 
   // ID of compute gyration
-  int n = strlen(arg[3]) + 1;
+  id_gyration_chunk = utils::strdup(arg[3]);
-  id_gyration_chunk = new char[n];
-  strcpy(id_gyration_chunk,arg[3]);
 
   init();
 

src/USER-MISC/compute_hma.cpp

@@ -78,11 +78,7 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   if (narg < 4) error->all(FLERR,"Illegal compute hma command");
   if (igroup) error->all(FLERR,"Compute hma must use group all");
   if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}
-  else {
+  else id_temp = utils::strdup(arg[3]);
-    int n = strlen(arg[3]) + 1;
-    id_temp = new char[n];
-    strcpy(id_temp,arg[3]);
-  }
 
   create_attribute = 1;
   extscalar = 1;
@@ -92,23 +88,11 @@ ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
   // our new fix's id (id_fix)= compute-ID + COMPUTE_STORE
   // our new fix's group = same as compute group
 
-  int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
+  id_fix = utils::strdup(std::string(id)+"_COMPUTE_STORE");
-  id_fix = new char[n];
+  modify->add_fix(fmt::format("{} {} STORE peratom 1 3",
-  strcpy(id_fix,id);
+                              id_fix, group->names[igroup]));
-  strcat(id_fix,"_COMPUTE_STORE");
-
-  char **newarg = new char*[6];
-  newarg[0] = id_fix;
-  newarg[1] = group->names[igroup];
-  newarg[2] = (char *) "STORE";
-  newarg[3] = (char *) "peratom";
-  newarg[4] = (char *) "1";
-  newarg[5] = (char *) "3";
-  modify->add_fix(6,newarg);
   fix = (FixStore *) modify->fix[modify->nfix-1];
 
-  delete [] newarg;
-
   // calculate xu,yu,zu for fix store array
   // skip if reset from restart file
 

src/USER-MISC/compute_pressure_grem.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_pressure_grem.h"
-#include <cstring>
+
 #include "update.h"
 #include "domain.h"
 #include "modify.h"
@@ -21,6 +21,8 @@
 #include "kspace.h"
 #include "error.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------
@@ -30,9 +32,7 @@ using namespace LAMMPS_NS;
 ComputePressureGrem::ComputePressureGrem(LAMMPS *lmp, int narg, char **arg) :
   ComputePressure(lmp, narg-1, arg)
 {
-  int len = strlen(arg[narg-1])+1;
+  fix_grem = utils::strdup(arg[narg-1]);
-  fix_grem = new char[len];
-  strcpy(fix_grem,arg[narg-1]);
 }
 
 /* ---------------------------------------------------------------------- */