Merge pull request #2674 from rbberger/small_changes

Small code changes

doc/src/fix_rigid_meso.rst

@@ -48,8 +48,8 @@ Examples
    fix 1 ellipsoid rigid/meso single
    fix 1 rods      rigid/meso molecule
    fix 1 spheres   rigid/meso single force 1 off off on
-   fix 1 particles rigid/meso molecule force 1\*5 off off off force 6\*10 off off on
+   fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
-   fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque \* off off off
+   fix 2 spheres   rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off
 
 Description
 """""""""""

doc/src/group.rst

@@ -120,12 +120,12 @@ specified atom types, atom IDs, or molecule IDs into the group.  These
 The first format is a list of values (types or IDs).  For example, the
 second command in the examples above puts all atoms of type 3 or 4 into
 the group named *water*\ .  Each entry in the list can be a
-colon-separated sequence A:B or A:B:C, as in two of the examples
+colon-separated sequence ``A:B`` or ``A:B:C``, as in two of the examples
 above.  A "sequence" generates a sequence of values (types or IDs),
-with an optional increment.  The first example with 500:1000 has the
+with an optional increment.  The first example with ``500:1000`` has the
 default increment of 1 and would add all atom IDs from 500 to 1000
 (inclusive) to the group sub, along with 10,25,50 since they also
-appear in the list of values.  The second example with 100:10000:10
+appear in the list of values.  The second example with ``100:10000:10``
 uses an increment of 10 and would thus would add atoms IDs
 100,110,120, ... 9990,10000 to the group sub.
 
@@ -269,7 +269,7 @@ group and running further.
 .. code-block:: LAMMPS
 
    variable        nsteps equal 5000
-   variable        rad equal 18-(step/v_nsteps)\*(18-5)
+   variable        rad equal 18-(step/v_nsteps)*(18-5)
    region          ss sphere 20 20 0 v_rad
    group           mobile dynamic all region ss
    fix             1 mobile nve

doc/src/kim_commands.rst

@@ -1205,7 +1205,7 @@ coordinates of atoms in the unit cell of the cubic crystal.  In the case of,
 e.g. a conventional fcc unit cell, the "source-value" key in the map associated
 with this key should be assigned the following value:
 
-.. code-block:: LAMMPS
+.. code-block:: text
 
    [[0.0, 0.0, 0.0],
     [0.5, 0.5, 0.0],

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -40,7 +40,7 @@ class LAMMPSLexer(RegexLexer):
             (r'compute\s+', Keyword, 'compute'),
             (r'dump\s+', Keyword, 'dump'),
             (r'region\s+', Keyword, 'region'),
-            (r'variable\s+', Keyword, 'variable'),
+            (r'^\s*variable\s+', Keyword, 'variable_cmd'),
             (r'group\s+', Keyword, 'group'),
             (r'change_box\s+', Keyword, 'change_box'),
             (r'uncompute\s+', Keyword, 'uncompute'),
@@ -51,6 +51,7 @@ class LAMMPSLexer(RegexLexer):
             (r'#.*?\n', Comment),
             ('"', String, 'string'),
             ('\'', String, 'single_quote_string'),
+            (r'[0-9]+:[0-9]+(:[0-9]+)?', Number),
             (r'[0-9]+(\.[0-9]+)?([eE]\-?[0-9]+)?', Number),
             ('\$?\(', Name.Variable, 'expression'),
             ('\$\{', Name.Variable, 'variable'),
@@ -58,6 +59,7 @@ class LAMMPSLexer(RegexLexer):
             (r'\$[\w_]+', Name.Variable),
             (r'\s+', Whitespace),
             (r'[\+\-\*\^\|\/\!%&=<>]', Operator),
+            (r'[\~\.\w_:,@\-\/\\0-9]+', Text),
         ],
         'keywords' : [
             (words(LAMMPS_COMMANDS, suffix=r'\b', prefix=r'^'), Keyword)
@@ -99,7 +101,7 @@ class LAMMPSLexer(RegexLexer):
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],
-        'variable' : [
+        'variable_cmd' : [
             (r'[\w_\-\.\[\]]+', Name.Variable.Identifier),
             default('#pop')
         ],

src/COMPRESS/dump_atom_gz.cpp

@@ -77,14 +77,12 @@ void DumpAtomGZ::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_atom_zstd.cpp

@@ -76,14 +76,12 @@ void DumpAtomZstd::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_cfg_gz.cpp

@@ -81,14 +81,12 @@ void DumpCFGGZ::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_cfg_zstd.cpp

@@ -79,14 +79,12 @@ void DumpCFGZstd::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_custom_gz.cpp

@@ -79,14 +79,12 @@ void DumpCustomGZ::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_custom_zstd.cpp

@@ -76,14 +76,12 @@ void DumpCustomZstd::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_local_gz.cpp

@@ -79,14 +79,12 @@ void DumpLocalGZ::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_local_zstd.cpp

@@ -78,14 +78,12 @@ void DumpLocalZstd::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_xyz_gz.cpp

@@ -78,14 +78,12 @@ void DumpXYZGZ::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/COMPRESS/dump_xyz_zstd.cpp

@@ -76,14 +76,12 @@ void DumpXYZZstd::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }

src/dump.cpp

@@ -46,20 +46,14 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);
 
-  int n = strlen(arg[0]) + 1;
+  id = utils::strdup(arg[0]);
-  id = new char[n];
-  strcpy(id,arg[0]);
 
   igroup = group->find(arg[1]);
   groupbit = group->bitmask[igroup];
 
-  n = strlen(arg[2]) + 1;
+  style = utils::strdup(arg[2]);
-  style = new char[n];
-  strcpy(style,arg[2]);
 
-  n = strlen(arg[4]) + 1;
+  filename = utils::strdup(arg[4]);
-  filename = new char[n];
-  strcpy(filename,arg[4]);
 
   comm_forward = comm_reverse = 0;
 
@@ -140,9 +134,8 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
     filewriter = 1;
     fileproc = me;
     MPI_Comm_split(world,me,0,&clustercomm);
-    multiname = new char[strlen(filename) + 16];
     *ptr = '\0';
-    sprintf(multiname,"%s%d%s",filename,me,ptr+1);
+    multiname = utils::strdup(fmt::format("{}{}{}", filename, me, ptr+1));
     *ptr = '%';
   }
 
@@ -573,14 +566,12 @@ void Dump::openfile()
     *ptr = '*';
     if (maxfiles > 0) {
       if (numfiles < maxfiles) {
-        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        nameslist[numfiles] = utils::strdup(filecurrent);
-        strcpy(nameslist[numfiles],filecurrent);
         ++numfiles;
       } else {
         remove(nameslist[fileidx]);
         delete[] nameslist[fileidx];
-        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        nameslist[fileidx] = utils::strdup(filecurrent);
-        strcpy(nameslist[fileidx],filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
       }
     }
@@ -952,9 +943,7 @@ void Dump::modify_params(int narg, char **arg)
       int n;
       if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
         delete [] output->var_dump[idump];
-        n = strlen(&arg[iarg+1][2]) + 1;
+        output->var_dump[idump] = utils::strdup(&arg[iarg+1][2]);
-        output->var_dump[idump] = new char[n];
-        strcpy(output->var_dump[idump],&arg[iarg+1][2]);
         n = 0;
       } else {
         n = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
@@ -984,10 +973,9 @@ void Dump::modify_params(int narg, char **arg)
       MPI_Comm_split(world,icluster,0,&clustercomm);
 
       delete [] multiname;
-      multiname = new char[strlen(filename) + 16];
       char *ptr = strchr(filename,'%');
       *ptr = '\0';
-      sprintf(multiname,"%s%d%s",filename,icluster,ptr+1);
+      multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
       *ptr = '%';
       iarg += 2;
 
@@ -1028,9 +1016,7 @@ void Dump::modify_params(int narg, char **arg)
 
       if (strcmp(arg[iarg+1],"line") == 0) {
         delete [] format_line_user;
-        int n = strlen(arg[iarg+2]) + 1;
+        format_line_user = utils::strdup(arg[iarg+2]);
-        format_line_user = new char[n];
-        strcpy(format_line_user,arg[iarg+2]);
         iarg += 3;
       } else {   // pass other format options to child classes
         int n = modify_param(narg-iarg,&arg[iarg]);
@@ -1085,10 +1071,9 @@ void Dump::modify_params(int narg, char **arg)
       MPI_Comm_split(world,icluster,0,&clustercomm);
 
       delete [] multiname;
-      multiname = new char[strlen(filename) + 16];
       char *ptr = strchr(filename,'%');
       *ptr = '\0';
-      sprintf(multiname,"%s%d%s",filename,icluster,ptr+1);
+      multiname = utils::strdup(fmt::format("{}{}{}", filename, icluster, ptr+1));
       *ptr = '%';
       iarg += 2;
 

src/dump_cfg.cpp

@@ -74,14 +74,10 @@ DumpCFG::DumpCFG(LAMMPS *lmp, int narg, char **arg) :
                  |ArgInfo::DNAME|ArgInfo::INAME);
 
     if (argi.get_dim() == 1) {
-      std::string newarg(std::to_string(earg[iarg][0]));
+      std::string newarg = fmt::format("{}_{}_{}", earg[iarg][0], argi.get_name(), argi.get_index1());
-      newarg += std::string("_") + argi.get_name();
+      auxname[i] = utils::strdup(newarg);
-      newarg += std::string("_") + std::to_string(argi.get_index1());
-      auxname[i] = new char[newarg.size()+1];
-      strcpy(auxname[i],newarg.c_str());
     } else {
-      auxname[i] = new char[strlen(earg[iarg]) + 1];
+      auxname[i] = utils::strdup(earg[iarg]);
-      strcpy(auxname[i],earg[iarg]);
     }
   }
 }

src/dump_custom.cpp

@@ -285,7 +285,7 @@ void DumpCustom::init_style()
     else if (vtype[i] == Dump::DOUBLE && format_float_user)
       vformat[i] = utils::strdup(std::string(format_float_user) + " ");
     else if (vtype[i] == Dump::BIGINT && format_bigint_user)
-      vformat[i] = utils::strdup(std::string(format_int_user) + " ");
+      vformat[i] = utils::strdup(std::string(format_bigint_user) + " ");
     else vformat[i] = utils::strdup(word + " ");
 
     // remove trailing blank on last column's format
@@ -1562,9 +1562,7 @@ int DumpCustom::add_compute(const char *id)
   delete [] compute;
   compute = new Compute*[ncompute+1];
 
-  int n = strlen(id) + 1;
+  id_compute[ncompute] = utils::strdup(id);
-  id_compute[ncompute] = new char[n];
-  strcpy(id_compute[ncompute],id);
   ncompute++;
   return ncompute-1;
 }
@@ -1587,9 +1585,7 @@ int DumpCustom::add_fix(const char *id)
   delete [] fix;
   fix = new Fix*[nfix+1];
 
-  int n = strlen(id) + 1;
+  id_fix[nfix] = utils::strdup(id);
-  id_fix[nfix] = new char[n];
-  strcpy(id_fix[nfix],id);
   nfix++;
   return nfix-1;
 }
@@ -1616,9 +1612,7 @@ int DumpCustom::add_variable(const char *id)
   vbuf = new double*[nvariable+1];
   for (int i = 0; i <= nvariable; i++) vbuf[i] = nullptr;
 
-  int n = strlen(id) + 1;
+  id_variable[nvariable] = utils::strdup(id);
-  id_variable[nvariable] = new char[n];
-  strcpy(id_variable[nvariable],id);
   nvariable++;
   return nvariable-1;
 }
@@ -1642,9 +1636,7 @@ int DumpCustom::add_custom(const char *id, int flag)
   flag_custom = (int *)
     memory->srealloc(flag_custom,(ncustom+1)*sizeof(int),"dump:flag_custom");
 
-  int n = strlen(id) + 1;
+  id_custom[ncustom] = utils::strdup(id);
-  id_custom[ncustom] = new char[n];
-  strcpy(id_custom[ncustom],id);
   flag_custom[ncustom] = flag;
 
   ncustom++;
@@ -1663,9 +1655,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       if (iregion == -1)
         error->all(FLERR,"Dump_modify region ID does not exist");
       delete [] idregion;
-      int n = strlen(arg[1]) + 1;
+      idregion = utils::strdup(arg[1]);
-      idregion = new char[n];
-      strcpy(idregion,arg[1]);
     }
     return 2;
   }
@@ -1686,11 +1676,9 @@ int DumpCustom::modify_param(int narg, char **arg)
 
     if (strcmp(arg[1],"int") == 0) {
       delete [] format_int_user;
-      int n = strlen(arg[2]) + 1;
+      format_int_user = utils::strdup(arg[2]);
-      format_int_user = new char[n];
-      strcpy(format_int_user,arg[2]);
       delete [] format_bigint_user;
-      n = strlen(format_int_user) + 8;
+      int n = strlen(format_int_user) + 8;
       format_bigint_user = new char[n];
       // replace "d" in format_int_user with bigint format specifier
       // use of &str[1] removes leading '%' from BIGINT_FORMAT string
@@ -1706,18 +1694,14 @@ int DumpCustom::modify_param(int narg, char **arg)
 
     } else if (strcmp(arg[1],"float") == 0) {
       delete [] format_float_user;
-      int n = strlen(arg[2]) + 1;
+      format_float_user = utils::strdup(arg[2]);
-      format_float_user = new char[n];
-      strcpy(format_float_user,arg[2]);
 
     } else {
       int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1;
       if (i < 0 || i >= nfield)
         error->all(FLERR,"Illegal dump_modify command");
       if (format_column_user[i]) delete [] format_column_user[i];
-      int n = strlen(arg[2]) + 1;
+      format_column_user[i] = utils::strdup(arg[2]);
-      format_column_user[i] = new char[n];
-      strcpy(format_column_user[i],arg[2]);
     }
     return 3;
   }
@@ -1730,9 +1714,7 @@ int DumpCustom::modify_param(int narg, char **arg)
     delete [] typenames;
     typenames = new char*[ntypes+1];
     for (int itype = 1; itype <= ntypes; itype++) {
-      int n = strlen(arg[itype]) + 1;
+      typenames[itype] = utils::strdup(arg[itype]);
-      typenames[itype] = new char[n];
-      strcpy(typenames[itype],arg[itype]);
     }
     return ntypes+1;
   }
@@ -1998,8 +1980,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       memory->grow(thresh_first,(nthreshlast+1),"dump:thresh_first");
 
       std::string threshid = fmt::format("{}{}_DUMP_STORE",id,nthreshlast);
-      thresh_fixID[nthreshlast] = new char[threshid.size()+1];
+      thresh_fixID[nthreshlast] = utils::strdup(threshid);
-      strcpy(thresh_fixID[nthreshlast],threshid.c_str());
       modify->add_fix(fmt::format("{} {} STORE peratom 1 1",threshid,
                                   group->names[igroup]));
       thresh_fix[nthreshlast] = (FixStore *) modify->fix[modify->nfix-1];

src/dump_local.cpp

@@ -472,9 +472,7 @@ int DumpLocal::add_compute(const char *id)
   delete [] compute;
   compute = new Compute*[ncompute+1];
 
-  int n = strlen(id) + 1;
+  id_compute[ncompute] = utils::strdup(id);
-  id_compute[ncompute] = new char[n];
-  strcpy(id_compute[ncompute],id);
   ncompute++;
   return ncompute-1;
 }
@@ -497,9 +495,7 @@ int DumpLocal::add_fix(const char *id)
   delete [] fix;
   fix = new Fix*[nfix+1];
 
-  int n = strlen(id) + 1;
+  id_fix[nfix] = utils::strdup(id);
-  id_fix[nfix] = new char[n];
-  strcpy(id_fix[nfix],id);
   nfix++;
   return nfix-1;
 }

src/dump_xyz.cpp

@@ -40,10 +40,7 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
 
   if (format_default) delete [] format_default;
 
-  char *str = (char *) "%s %g %g %g";
+  format_default = utils::strdup("%s %g %g %g");
-  int n = strlen(str) + 1;
-  format_default = new char[n];
-  strcpy(format_default,str);
 
   ntypes = atom->ntypes;
   typenames = nullptr;
@@ -71,14 +68,11 @@ void DumpXYZ::init_style()
   // format = copy of default or user-specified line format
 
   delete [] format;
-  char *str;
-  if (format_line_user) str = format_line_user;
-  else str = format_default;
 
-  int n = strlen(str) + 2;
+  if (format_line_user)
-  format = new char[n];
+    format = utils::strdup(fmt::format("{}\n", format_line_user));
-  strcpy(format,str);
+  else
-  strcat(format,"\n");
+    format = utils::strdup(fmt::format("{}\n", format_default));
 
   // initialize typenames array to be backward compatible by default
   // a 32-bit int can be maximally 10 digits plus sign
@@ -119,9 +113,7 @@ int DumpXYZ::modify_param(int narg, char **arg)
 
     typenames = new char*[ntypes+1];
     for (int itype = 1; itype <= ntypes; itype++) {
-      int n = strlen(arg[itype]) + 1;
+      typenames[itype] = utils::strdup(arg[itype]);
-      typenames[itype] = new char[n];
-      strcpy(typenames[itype],arg[itype]);
     }
 
     return ntypes+1;

src/tokenizer.cpp

@@ -35,12 +35,14 @@ TokenizerException::TokenizerException(const std::string &msg, const std::string
 /** Class for splitting text into words
  *
  * This tokenizer will break down a string into sub-strings (i.e words)
- * separated by the given separator characters.
+ * separated by the given separator characters. If the string contains
+ * certain known UTF-8 characters they will be replaced by their ASCII
+ * equivalents processing the string.
  *
 \verbatim embed:rst
 
 *See also*
-   :cpp:class:`ValueTokenizer`, :cpp:func:`utils::split_words`
+   :cpp:class:`ValueTokenizer`, :cpp:func:`utils::split_words`, :cpp:func:`utils::utf8_subst`
 
 \endverbatim
  *
@@ -50,6 +52,8 @@ TokenizerException::TokenizerException(const std::string &msg, const std::string
 Tokenizer::Tokenizer(const std::string &str, const std::string &separators) :
     text(str), separators(separators), start(0), ntokens(std::string::npos)
 {
+    // replace known UTF-8 characters with ASCII equivalents
+    if (utils::has_utf8(text)) text = utils::utf8_subst(text);
     reset();
 }
 
@@ -197,70 +201,51 @@ bool ValueTokenizer::contains(const std::string &value) const {
  *
  * \return   string with next token */
 std::string ValueTokenizer::next_string() {
-    if (has_next()) {
+    return tokens.next();
-        std::string value = tokens.next();
-        return value;
-    } throw TokenizerException("Not enough tokens","");
 }
 
 /*! Retrieve next token and convert to int
  *
  * \return   value of next token */
 int ValueTokenizer::next_int() {
-    if (has_next()) {
+    std::string current = tokens.next();
-        std::string current = tokens.next();
+    if (!utils::is_integer(current)) {
-        if (utils::has_utf8(current)) current = utils::utf8_subst(current);
+        throw InvalidIntegerException(current);
-        if (!utils::is_integer(current)) {
+    }
-            throw InvalidIntegerException(current);
+    return atoi(current.c_str());
-        }
-        int value = atoi(current.c_str());
-        return value;
-    } throw TokenizerException("Not enough tokens","");
 }
 
 /*! Retrieve next token and convert to bigint
  *
  * \return   value of next token */
 bigint ValueTokenizer::next_bigint() {
-    if (has_next()) {
+    std::string current = tokens.next();
-        std::string current = tokens.next();
+    if (!utils::is_integer(current)) {
-        if (utils::has_utf8(current)) current = utils::utf8_subst(current);
+        throw InvalidIntegerException(current);
-        if (!utils::is_integer(current)) {
+    }
-            throw InvalidIntegerException(current);
+    return ATOBIGINT(current.c_str());
-        }
-        bigint value = ATOBIGINT(current.c_str());
-        return value;
-    } throw TokenizerException("Not enough tokens","");
 }
 
 /*! Retrieve next token and convert to tagint
  *
  * \return   value of next token */
 tagint ValueTokenizer::next_tagint() {
-    if (has_next()) {
+    std::string current = tokens.next();
-        std::string current = tokens.next();
+    if (!utils::is_integer(current)) {
-        if (utils::has_utf8(current)) current = utils::utf8_subst(current);
+        throw InvalidIntegerException(current);
-        if (!utils::is_integer(current)) {
+    }
-            throw InvalidIntegerException(current);
+    return ATOTAGINT(current.c_str());
-        }
-        tagint value = ATOTAGINT(current.c_str());
-        return value;
-    } throw TokenizerException("Not enough tokens","");
 }
 
 /*! Retrieve next token and convert to double
  *
  * \return   value of next token */
 double ValueTokenizer::next_double() {
-    if (has_next()) {
+    std::string current = tokens.next();
-        std::string current = tokens.next();
+    if (!utils::is_double(current)) {
-        if (utils::has_utf8(current)) current = utils::utf8_subst(current);
+        throw InvalidFloatException(current);
-        if (!utils::is_double(current)) {
+    }
-            throw InvalidFloatException(current);
+    return atof(current.c_str());
-        }
-        double value = atof(current.c_str());
-        return value;
-    } throw TokenizerException("Not enough tokens","");
 }
 
 /*! Skip over a given number of tokens