diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp
index eadff698cb..33a81db748 100644
--- a/src/tokenizer.cpp
+++ b/src/tokenizer.cpp
@@ -17,7 +17,9 @@
 
 #include "tokenizer.h"
 #include "utils.h"
-#include <algorithm>
+#include <exception>
+#include <utility>
+
 #include "fmt/format.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/universe.cpp b/src/universe.cpp
index e920270c1e..acb5100337 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -12,16 +12,14 @@
 ------------------------------------------------------------------------- */
 
 #include "universe.h"
-#include <mpi.h>
-#include <cctype>
-#include <cstdlib>
-#include <cstring>
-#include "version.h"
+
 #include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "version.h"
+
+#include <cctype>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/update.cpp b/src/update.cpp
index a1c712c354..399584473c 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -15,8 +15,8 @@
 #include <cstring>
 #include "integrate.h"
 #include "min.h"
-#include "style_integrate.h"
-#include "style_minimize.h"
+#include "style_integrate.h"  // IWYU pragma: keep
+#include "style_minimize.h"   // IWYU pragma: keep
 #include "neighbor.h"
 #include "force.h"
 #include "modify.h"
@@ -61,7 +61,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
 #define INTEGRATE_CLASS
 #define IntegrateStyle(key,Class) \
   (*integrate_map)[#key] = &integrate_creator<Class>;
-#include "style_integrate.h"
+#include "style_integrate.h"   // IWYU pragma: keep
 #undef IntegrateStyle
 #undef INTEGRATE_CLASS
 
@@ -70,7 +70,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
 #define MINIMIZE_CLASS
 #define MinimizeStyle(key,Class) \
   (*minimize_map)[#key] = &minimize_creator<Class>;
-#include "style_minimize.h"
+#include "style_minimize.h"    // IWYU pragma: keep
 #undef MinimizeStyle
 #undef MINIMIZE_CLASS
 
diff --git a/src/update.h b/src/update.h
index e70325a498..558719f4cc 100644
--- a/src/update.h
+++ b/src/update.h
@@ -15,8 +15,8 @@
 #define LMP_UPDATE_H
 
 #include "pointers.h"
+
 #include <map>
-#include <string>
 
 namespace LAMMPS_NS {
 
diff --git a/src/utils.cpp b/src/utils.cpp
index 45bd629c19..c3a6d1e480 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -12,20 +12,20 @@
 ------------------------------------------------------------------------- */
 
 #include "utils.h"
-#include <cstring>
-#include <cstdlib>
-#include <cerrno>
-#include "lammps.h"
+
 #include "comm.h"
 #include "compute.h"
 #include "error.h"
 #include "fix.h"
 #include "memory.h"
 #include "modify.h"
-#include "tokenizer.h"
 #include "text_file_reader.h"
+#include "tokenizer.h"
 #include "update.h"
-#include "fmt/format.h"
+
+#include <cctype>
+#include <cerrno>
+#include <cstring>
 
 #if defined(__linux__)
 #include <unistd.h>  // for readlink
diff --git a/src/variable.cpp b/src/variable.cpp
index d16987984f..8d4416dfa7 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -12,36 +12,33 @@
 ------------------------------------------------------------------------- */
 
 #include "variable.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstdlib>
-#include <cstring>
-#include <cctype>
-#include <unistd.h>
-#include <string>
-#include "universe.h"
+
 #include "atom.h"
-#include "update.h"
-#include "group.h"
-#include "domain.h"
 #include "comm.h"
-#include "region.h"
-#include "modify.h"
 #include "compute.h"
-#include "input.h"
+#include "domain.h"
+#include "error.h"
 #include "fix.h"
 #include "fix_store.h"
-#include "force.h"
-#include "output.h"
-#include "thermo.h"
-#include "random_mars.h"
-#include "math_const.h"
-#include "lmppython.h"
-#include "memory.h"
+#include "group.h"
 #include "info.h"
-#include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "input.h"
+#include "lmppython.h"
+#include "math_const.h"
+#include "memory.h"
+#include "modify.h"
+#include "output.h"
+#include "random_mars.h"
+#include "region.h"
+#include "thermo.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cctype>
+#include <cmath>
+#include <cstring>
+#include <unistd.h>
+#include <vector>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/variable.h b/src/variable.h
index f5ea11c0b4..efffacc7bb 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -15,7 +15,6 @@
 #define LMP_VARIABLE_H
 
 #include "pointers.h"
-#include <string>
 
 namespace LAMMPS_NS {
 
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 140a396926..eafa98cb7c 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -12,24 +12,24 @@
 ------------------------------------------------------------------------- */
 
 #include "velocity.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
-#include "domain.h"
-#include "lattice.h"
-#include "input.h"
-#include "variable.h"
-#include "force.h"
-#include "modify.h"
-#include "fix.h"
+#include "comm.h"
 #include "compute.h"
 #include "compute_temp.h"
-#include "random_park.h"
-#include "group.h"
-#include "comm.h"
-#include "memory.h"
+#include "domain.h"
 #include "error.h"
-#include "utils.h"
+#include "fix.h"
+#include "group.h"
+#include "input.h"
+#include "lattice.h"
+#include "memory.h"
+#include "modify.h"
+#include "random_park.h"
+#include "variable.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 97c5f918b5..a7b9ba4c22 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -12,26 +12,26 @@
 ------------------------------------------------------------------------- */
 
 #include "verlet.h"
-#include <cstring>
-#include <string>
-#include "neighbor.h"
-#include "domain.h"
-#include "comm.h"
+
+#include "angle.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "force.h"
-#include "pair.h"
 #include "bond.h"
-#include "angle.h"
+#include "comm.h"
 #include "dihedral.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "improper.h"
 #include "kspace.h"
-#include "output.h"
-#include "update.h"
 #include "modify.h"
+#include "neighbor.h"
+#include "output.h"
+#include "pair.h"
 #include "timer.h"
-#include "error.h"
-#include "fmt/format.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index 612f5bb123..121a2ed1fd 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -12,22 +12,21 @@
 ------------------------------------------------------------------------- */
 
 #include "write_coeff.h"
-#include <cstring>
-#include <cstdlib>
-#include <cctype>
-#include <unistd.h>
-#include "pair.h"
-#include "bond.h"
+
 #include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
+#include "bond.h"
 #include "comm.h"
-#include "force.h"
-#include "universe.h"
-#include "error.h"
+#include "dihedral.h"
 #include "domain.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "error.h"
+#include "force.h"
+#include "improper.h"
+#include "pair.h"
+#include "universe.h"
+
+#include <cctype>
+#include <cstring>
+#include <unistd.h>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/write_data.h b/src/write_data.h
index e94e7f5595..a4e71c9cda 100644
--- a/src/write_data.h
+++ b/src/write_data.h
@@ -21,7 +21,6 @@ CommandStyle(write_data,WriteData)
 #define LMP_WRITE_DATA_H
 
 #include "pointers.h"
-#include <string>
 
 namespace LAMMPS_NS {
 
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index 9b257b9ab0..56839a2f5e 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -16,15 +16,16 @@
 ------------------------------------------------------------------------- */
 
 #include "write_dump.h"
-#include <cstring>
-#include <string>
 #include "style_dump.h"
+
+#include "comm.h"
 #include "dump.h"
 #include "dump_image.h"
-#include "comm.h"
-#include "update.h"
 #include "error.h"
-#include "utils.h"
+#include "update.h"
+
+#include <cstring>
+
 
 using namespace LAMMPS_NS;
 
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 22e993c37c..256d7a377e 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -12,32 +12,30 @@
 ------------------------------------------------------------------------- */
 
 #include "write_restart.h"
-#include <mpi.h>
-#include <cstring>
-#include <string>
+
+#include "angle.h"
 #include "atom.h"
 #include "atom_vec.h"
-#include "group.h"
-#include "force.h"
-#include "pair.h"
 #include "bond.h"
-#include "angle.h"
-#include "dihedral.h"
-#include "improper.h"
-#include "update.h"
-#include "neighbor.h"
-#include "domain.h"
-#include "modify.h"
-#include "fix.h"
-#include "universe.h"
 #include "comm.h"
-#include "output.h"
-#include "thermo.h"
-#include "mpiio.h"
-#include "memory.h"
+#include "dihedral.h"
+#include "domain.h"
 #include "error.h"
-#include "utils.h"
-#include "fmt/format.h"
+#include "fix.h"
+#include "force.h"
+#include "group.h"
+#include "improper.h"
+#include "memory.h"
+#include "modify.h"
+#include "mpiio.h"
+#include "neighbor.h"
+#include "output.h"
+#include "pair.h"
+#include "thermo.h"
+#include "universe.h"
+#include "update.h"
+
+#include <cstring>
 
 #include "lmprestart.h"
 
diff --git a/src/write_restart.h b/src/write_restart.h
index 5056f50636..a4a606482e 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -21,7 +21,6 @@ CommandStyle(write_restart,WriteRestart)
 #define LMP_WRITE_RESTART_H
 
 #include "pointers.h"
-#include <string>
 
 namespace LAMMPS_NS {