diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index 9ed591f73f..38cc372e22 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -13,21 +13,23 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_bond_local.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec.h"
-#include "molecule.h"
-#include "update.h"
-#include "domain.h"
-#include "force.h"
 #include "bond.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "input.h"
-#include "variable.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "molecule.h"
+#include "update.h"
+#include "variable.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -81,7 +83,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
       vstr[nvar] = utils::strdup(&arg[iarg][2]);
       nvar++;
     } else if (arg[iarg][0] == 'b') {
-      int n = atoi(&arg[iarg][1]);
+      int n = std::stoi(&arg[iarg][1]);
       if (n <= 0) error->all(FLERR, "Invalid keyword {} in compute bond/local command", arg[iarg]);
       bstyle[nvalues] = BN;
       bindex[nvalues++] = n - 1;
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 88991f7481..ac6a3bfb99 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -67,7 +67,7 @@ ComputePairLocal::ComputePairLocal(LAMMPS *lmp, int narg, char **arg) :
     else if (strcmp(arg[iarg], "dz") == 0)
       pstyle[nvalues++] = DZ;
     else if (arg[iarg][0] == 'p') {
-      int n = atoi(&arg[iarg][1]);
+      int n = std::stoi(&arg[iarg][1]);
       if (n <= 0) error->all(FLERR, "Invalid keyword {} in compute pair/local command", arg[iarg]);
       pstyle[nvalues] = PN;
       pindex[nvalues++] = n - 1;
diff --git a/src/lammps.cpp b/src/lammps.cpp
index b3659fdf50..8e81f785de 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -191,7 +191,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
     int me,nprocs;
     MPI_Comm_rank(communicator,&me);
     MPI_Comm_size(communicator,&nprocs);
-    int color = atoi(arg[iarg+1]);
+    int color = std::stoi(arg[iarg+1]);
     MPI_Comm subcomm;
     MPI_Comm_split(communicator,color,me,&subcomm);
     external_comm = communicator;
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index 10d16ac859..f252e01644 100644
--- a/src/reader_native.cpp
+++ b/src/reader_native.cpp
@@ -484,7 +484,7 @@ void ReaderNative::read_atoms(int n, int nfield, double **fields)
       // convert selected fields to floats
 
       for (int m = 0; m < nfield; m++)
-        fields[i][m] = atof(words[fieldindex[m]].c_str());
+        fields[i][m] = std::stod(words[fieldindex[m]]);
     }
   }
 }
diff --git a/src/universe.cpp b/src/universe.cpp
index edd5b01031..fb07e26759 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -181,10 +181,10 @@ void Universe::add_world(char *str)
       if ((found == 0) || (found == (part.size() - 1))) {
         valid = false;
       } else if (found == std::string::npos) {
-        nper = atoi(part.c_str());
+        nper = std::stoi(part);
       } else {
-        n = atoi(part.substr(0,found).c_str());
-        nper = atoi(part.substr(found+1).c_str());
+        n = std::stoi(part.substr(0,found));
+        nper = std::stoi(part.substr(found+1));
       }
     }
 
@@ -193,8 +193,7 @@ void Universe::add_world(char *str)
     if (n < 1 || nper < 1) valid = false;
 
     if (!valid)
-      error->universe_all(FLERR,fmt::format("Invalid partition string '{}'",
-                                            str));
+      error->universe_all(FLERR, fmt::format("Invalid partition string '{}'", str));
   } else nper = nprocs;
 
   memory->grow(procs_per_world,nworlds+n,"universe:procs_per_world");
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index 11987d4b37..5a7177f62f 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -152,7 +152,7 @@ void WriteCoeff::command(int narg, char **arg)
           }
 
           // parse type number and skip over it
-          int type = atoi(str);
+          int type = std::stoi(str);
           char *p = str;
           while ((*p != '\0') && (*p == ' ')) ++p;
           while ((*p != '\0') && isdigit(*p)) ++p;