use portable functions from platform and utils namespaces

src/COLVARS/fix_colvars.cpp

@@ -303,7 +303,7 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
   me = comm->me;
   root2root = MPI_COMM_NULL;
 
-  conf_file = strdup(arg[3]);
+  conf_file = utils::strdup(arg[3]);
   rng_seed = 1966;
   unwrap_flag = 1;
 
@@ -319,22 +319,22 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
       error->all(FLERR,"Missing argument to keyword");
 
     if (0 == strcmp(arg[iarg], "input")) {
-      inp_name = strdup(arg[iarg+1]);
+      inp_name = utils::strdup(arg[iarg+1]);
     } else if (0 == strcmp(arg[iarg], "output")) {
-      out_name = strdup(arg[iarg+1]);
+      out_name = utils::strdup(arg[iarg+1]);
     } else if (0 == strcmp(arg[iarg], "seed")) {
       rng_seed = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
     } else if (0 == strcmp(arg[iarg], "unwrap")) {
       unwrap_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
     } else if (0 == strcmp(arg[iarg], "tstat")) {
-      tmp_name = strdup(arg[iarg+1]);
+      tmp_name = utils::strdup(arg[iarg+1]);
     } else {
       error->all(FLERR,"Unknown fix colvars parameter");
     }
     ++iarg; ++iarg;
   }
 
-  if (!out_name) out_name = strdup("out");
+  if (!out_name) out_name = utils::strdup("out");
 
   /* initialize various state variables. */
   tstat_id = -1;
@@ -359,10 +359,10 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
 
 FixColvars::~FixColvars()
 {
-  memory->sfree(conf_file);
-  memory->sfree(inp_name);
-  memory->sfree(out_name);
-  memory->sfree(tmp_name);
+  delete[] conf_file;
+  delete[] inp_name;
+  delete[] out_name;
+  delete[] tmp_name;
   memory->sfree(comm_buf);
 
   if (proxy) {
@@ -430,17 +430,15 @@ void FixColvars::one_time_init()
   // create and initialize the colvars proxy
 
   if (me == 0) {
-    if (screen) fputs("colvars: Creating proxy instance\n",screen);
-    if (logfile) fputs("colvars: Creating proxy instance\n",logfile);
+    utils::logmesg(lmp,"colvars: Creating proxy instance\n");
 
 #ifdef LAMMPS_BIGBIG
-    if (screen) fputs("colvars: cannot handle atom ids > 2147483647\n",screen);
-    if (logfile) fputs("colvars: cannot handle atom ids > 2147483647\n",logfile);
+    utils::logmesg(lmp,"colvars: cannot handle atom ids > 2147483647\n");
 #endif
 
     if (inp_name) {
       if (strcmp(inp_name,"NULL") == 0) {
-        memory->sfree(inp_name);
+        delete[] inp_name;
         inp_name = nullptr;
       }
     }
@@ -458,8 +456,7 @@ void FixColvars::one_time_init()
       }
     }
 
-    proxy = new colvarproxy_lammps(lmp,inp_name,out_name,
-                                   rng_seed,t_target,root2root);
+    proxy = new colvarproxy_lammps(lmp,inp_name,out_name,rng_seed,t_target,root2root);
     proxy->init(conf_file);
 
     num_coords = (proxy->modify_atom_positions()->size());

src/DPD-MESO/pair_mdpd.cpp

@@ -19,19 +19,19 @@
 
 #include "pair_mdpd.h"
 
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "random_mars.h"
+#include "update.h"
+
 #include <cmath>
 #include <ctime>
-#include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "random_mars.h"
-#include "citeme.h"
-#include "memory.h"
-#include "error.h"
-
 
 using namespace LAMMPS_NS;
 
@@ -218,11 +218,9 @@ void PairMDPD::settings(int narg, char **arg)
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  if (seed <= 0) {
-    struct timespec time;
-    clock_gettime( CLOCK_REALTIME, &time );
-    seed = time.tv_nsec;  // if seed is non-positive, get the current time as the seed
-  }
+  if (seed <= 0)
+    seed = (int) (platform::walltime() * 1073741824.0);
+
   delete random;
   random = new RanMars(lmp,(seed + comm->me) % 900000000);
 

src/DPD-MESO/pair_tdpd.cpp

@@ -18,19 +18,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tdpd.h"
-#include <cmath>
-#include <ctime>
-#include "atom.h"
-#include "comm.h"
-#include "update.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "random_mars.h"
-#include "citeme.h"
-#include "memory.h"
-#include "error.h"
 
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "random_mars.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
@@ -240,11 +240,9 @@ void PairTDPD::settings(int narg, char **arg)
 
   // initialize Marsaglia RNG with processor-unique seed
 
-  if (seed <= 0) {
-    struct timespec time;
-    clock_gettime( CLOCK_REALTIME, &time );
-    seed = time.tv_nsec;  // if seed is non-positive, get the current time as the seed
-  }
+  if (seed <= 0)
+    seed = (int) (platform::walltime() * 1073741824.0);
+
   delete random;
   random = new RanMars(lmp,(seed + comm->me) % 900000000);
 

src/EXTRA-FIX/fix_tmd.cpp

@@ -495,7 +495,7 @@ void FixTMD::readfile(char *file)
   delete [] buffer;
 
   if (me == 0) {
-    if (compressed) pclose(fp);
+    if (compressed) platform::pclose(fp);
     else fclose(fp);
   }
 

src/REAXFF/reaxff_ffield.cpp

@@ -32,7 +32,6 @@
 #include "text_file_reader.h"
 #include "utils.h"
 
-#include <cctype>
 #include <cmath>
 #include <cstring>
 #include <exception>
@@ -161,11 +160,10 @@ namespace ReaxFF {
           if (values.count() < 9)
             THROW_ERROR("Invalid force field file format");
 
-          auto element = values.next_string();
-          int len = MIN(element.size(),3); // truncate stored element symbol if necessary
-          for (j = 0; j < len; ++j)
-            sbp[i].name[j] = toupper(element[j]);
-          sbp[i].name[len] = '\0';
+          // copy element symbol in uppercase and truncate stored element symbol if necessary
+          auto element = utils::uppercase(values.next_string());
+          strncpy(sbp[i].name,element.c_str(),4);
+          sbp[i].name[4] = '\0';
 
           sbp[i].r_s        = values.next_double();
           sbp[i].valency    = values.next_double();

src/REPLICA/neb.cpp

@@ -528,12 +528,12 @@ void NEB::readfile(char *file, int flag)
 
   if (flag == 0) {
     if (me_universe == 0) {
-      if (compressed) pclose(fp);
+      if (compressed) platform::pclose(fp);
       else fclose(fp);
     }
   } else {
     if (me == 0 && ireplica) {
-      if (compressed) pclose(fp);
+      if (compressed) platform::pclose(fp);
       else fclose(fp);
     }
   }