diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp
index a876ac9dc7..ca3923d278 100644
--- a/src/BODY/fix_nph_body.cpp
+++ b/src/BODY/fix_nph_body.cpp
@@ -18,11 +18,8 @@
 #include "fix_nph_body.h"
 
 #include "error.h"
-#include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp
index bc669fc971..3aacfe7f65 100644
--- a/src/BODY/fix_npt_body.cpp
+++ b/src/BODY/fix_npt_body.cpp
@@ -18,11 +18,8 @@
 #include "fix_npt_body.h"
 
 #include "error.h"
-#include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp
index 442aed2c94..6209e1db2f 100644
--- a/src/BODY/fix_nvt_body.cpp
+++ b/src/BODY/fix_nvt_body.cpp
@@ -21,8 +21,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 027c0dbd5a..25e3afb31d 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -16,18 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_wall_body_polygon.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_rounded_polygon.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp
index 3ec0e4bbe6..68321f3b70 100644
--- a/src/BODY/pair_body_nparticle.cpp
+++ b/src/BODY/pair_body_nparticle.cpp
@@ -12,18 +12,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_body_nparticle.h"
-#include <cmath>
-#include <cstring>
-#include "math_extra.h"
+
 #include "atom.h"
 #include "atom_vec_body.h"
 #include "body_nparticle.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index 36074a1a21..5b1a4e4e83 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -16,13 +16,14 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_colloid.h"
-#include <cmath>
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
 #include "error.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h
index af91572d8e..669931399b 100644
--- a/src/COMPRESS/gz_file_writer.h
+++ b/src/COMPRESS/gz_file_writer.h
@@ -19,9 +19,10 @@
 #define LMP_GZ_FILE_WRITER_H
 
 #include "file_writer.h"
+
+#include <exception>
 #include <string>
 #include <zlib.h>
-#include <exception>
 
 namespace LAMMPS_NS {
 
@@ -40,8 +41,6 @@ public:
 
     void setCompressionLevel(int level);
 };
-
-
 }
 
 #endif
diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h
index 8980666856..030a01690a 100644
--- a/src/COMPRESS/zstd_file_writer.h
+++ b/src/COMPRESS/zstd_file_writer.h
@@ -21,9 +21,9 @@
 #define LMP_ZSTD_FILE_WRITER_H
 
 #include "file_writer.h"
+
 #include <string>
 #include <zstd.h>
-#include <exception>
 
 namespace LAMMPS_NS {
 
@@ -47,8 +47,6 @@ public:
     void setCompressionLevel(int level);
     void setChecksum(bool enabled);
 };
-
-
 }
 
 #endif
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 95c3df7b09..5782ff5969 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -16,28 +16,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_long_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index dbd55ef041..5b27e96cbd 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -16,28 +16,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 9663c4be51..0c3e36265f 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_wolf_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 8db3761f1f..1cd91e2d61 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_coul_wolf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index 3454adda18..f7d383b528 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_born_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index ec002289f2..fe3e8f092c 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 913f68f4c4..0c23141060 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 4f091eede5..81bd987850 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_buck_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 070b103ddf..d5391aeede 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -16,26 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_colloid_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index fc4a44adc4..ef9b2dff4d 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 1104175046..ca5cb7df9a 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_debye_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 85cd978f33..d988a47681 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_dsf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index 84b6a665db..f924f2c925 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_long_cs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 #define EWALD_F   1.12837917
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index d27b4650ba..e1d51b1359 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index 884834d94a..f66fc6d594 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_dpd_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "random_mars.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index 507461fd23..957bb938f3 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_dpd_tstat_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "random_mars.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index add3a3ca7a..fe2cc92450 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -16,23 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_alloy_gpu.h"
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "gpu_extra.h"
 #include "domain.h"
-
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "potential_file_reader.h"
 #include "suffix.h"
 #include "tokenizer.h"
-#include "potential_file_reader.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -389,7 +389,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
       ValueTokenizer values = reader.next_values(1);
       file->nelements = values.next_int();
 
-      if (values.count() != file->nelements + 1)
+      if ((int)values.count() != file->nelements + 1)
         error->one(FLERR,"Incorrect element names in EAM potential file");
 
       file->elements = new char*[file->nelements];
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index 394b520a73..b92e348ddf 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -16,23 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_fs_gpu.h"
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "gpu_extra.h"
 #include "domain.h"
-#include "suffix.h"
-
-#include "tokenizer.h"
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "potential_file_reader.h"
+#include "suffix.h"
+#include "tokenizer.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -388,7 +388,7 @@ void PairEAMFSGPU::read_file(char *filename)
       ValueTokenizer values = reader.next_values(1);
       file->nelements = values.next_int();
 
-      if (values.count() != file->nelements + 1)
+      if ((int)values.count() != file->nelements + 1)
         error->one(FLERR,"Incorrect element names in EAM potential file");
 
       file->elements = new char*[file->nelements];
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index fada4febb5..2ed72a3b08 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -16,22 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_eam_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
 #include "domain.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
-#include "neigh_request.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MAXLINE 1024
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index 04fc65dd06..8431ce1b67 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_gauss_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index c5e0a1afb5..d7adb5c657 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -16,28 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_gayberne_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 33774078d5..016147cb6e 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj96_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp
index 4d8d67cdca..a40da25da8 100644
--- a/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp
@@ -15,23 +15,18 @@
    Contributing author: Mike Brown (SNL)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
 #include "pair_lj_charmm_coul_charmm_gpu.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
@@ -205,8 +200,8 @@ double PairLJCharmmCoulCharmmGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJCharmmCoulCharmmGPU::cpu_compute(int start, int inum, int eflag,
-                                          int vflag, int *ilist,
-                                          int *numneigh, int **firstneigh)
+                                            int /* vflag */, int *ilist,
+                                            int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index 42e869207e..1fc8ba1c5f 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_charmm_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index ae5321bc4f..87dda4f190 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_class2_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index e32561ab59..4e224cb2d3 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -18,20 +18,14 @@
 #include "pair_lj_class2_gpu.h"
 
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "gpu_extra.h"
-#include "integrate.h"
-#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "suffix.h"
-#include "universe.h"
-#include "update.h"
 
 #include <cmath>
 
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 73839bdbed..1c9b9a0820 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -18,23 +18,16 @@
 #include "pair_lj_cubic_gpu.h"
 
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "gpu_extra.h"
-#include "integrate.h"
-#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "suffix.h"
-#include "universe.h"
-#include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 #include "pair_lj_cubic_const.h"
 
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 1583395f82..0a1076aef8 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index d83678bd9f..75a16ae210 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_debye_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index 3a29d7e5a2..e3500ce60d 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -17,25 +17,19 @@
 
 #include "pair_lj_cut_coul_dsf_gpu.h"
 #include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 34e31fc044..3ac52c08c5 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 2fd1d55b54..f92c83bcf7 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_coul_msm_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index 93af562ed0..b15822bde9 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -16,25 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index 9ec2bec258..d9d38d4cb0 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -16,27 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_dipole_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "kspace.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "math_const.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 1de70701f0..65fed01321 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index c63d1a4e91..67dcd6d0b6 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -15,30 +15,24 @@
    Contributing author: Vsevolod Nikolskiy (HSE)
 ------------------------------------------------------------------------- */
 
-#include <cmath>
-#include <cstdio>
-
-#include <cstring>
 #include "pair_lj_cut_tip4p_long_gpu.h"
-#include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
-#include "domain.h"
-#include "kspace.h"
+
 #include "angle.h"
+#include "atom.h"
 #include "bond.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index af042bef42..d5a23507ae 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_expand_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 87605af1a4..234173651d 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_expand_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index b45d757ef4..df5d6aee89 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -16,27 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_gromacs_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 97b53fec33..5b7cb1fa67 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sdk_coul_long_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
-#include "kspace.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
 #define A1        0.254829592
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index cd6f4bc544..1cfacfde83 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sdk_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index cb7a889ed5..033c0c1d62 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -16,25 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_lj_sf_dipole_sf_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index e72c12da79..f2cfbc2637 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_mie_cut_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index 507edd33f4..024346afb2 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_morse_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index 90a7af1d0e..18817bf551 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -16,28 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_resquared_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
-#include "math_extra.h"
 #include "atom.h"
-#include "atom_vec.h"
 #include "atom_vec_ellipsoid.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
 #include "domain.h"
-#include "update.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index 66bd6deb8f..0c963e947c 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -16,27 +16,20 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_soft_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
 #include "math_const.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index b819580488..1603704b9b 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_sw_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index 6c5bb48e26..fb1a130398 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -16,30 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_table_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
-#define LOOKUP 0
-#define LINEAR 1
-#define SPLINE 2
-#define BITMAP 3
+#include <cmath>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index c2f3413d3d..55576de4ec 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
 #include "memory.h"
 #include "neighbor.h"
 #include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
-#include "domain.h"
-#include "gpu_extra.h"
+#include "neigh_request.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index 6a5e9892ec..5d79a68af4 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_mod_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index 0c56212fef..9594845fd0 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_zbl_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 47a32f7fc2..cdf53d6cc6 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -18,26 +18,19 @@
  ------------------------------------------------------------------------- */
 
 #include "pair_ufm_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index b3c703952f..4c47b66b4a 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -16,22 +16,17 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_vashishta_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "neighbor.h"
-#include "neigh_request.h"
-#include "force.h"
 #include "comm.h"
-#include "memory.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "memory.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
 using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 3ac5f6c693..4e4e555134 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_colloid_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 8558b57cd8..104adef8d5 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -16,26 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_yukawa_gpu.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 97a859a5bf..267b9252bd 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -16,27 +16,19 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_zbl_gpu.h"
-#include "lmptype.h"
-#include <cmath>
-#include <cstdio>
 
-#include <cstring>
 #include "atom.h"
-#include "atom_vec.h"
-#include "comm.h"
-#include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "integrate.h"
-#include "memory.h"
-#include "error.h"
-#include "neigh_request.h"
-#include "universe.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 // External functions from cuda library for atom decomposition
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index 6a05be4e6f..a21bbb0999 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -20,11 +20,12 @@
 ------------------------------------------------------------------------- */
 
 #include "fft3d.h"
-#include <mpi.h>
-#include <cstdio>
+
+#include "remap.h"
+
 #include <cstdlib>
 #include <cmath>
-#include "remap.h"
+
 #if defined(_OPENMP)
 #include <omp.h>
 #endif
diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp
index 6123aedfb8..d61db8db96 100644
--- a/src/KSPACE/msm_cg.cpp
+++ b/src/KSPACE/msm_cg.cpp
@@ -16,9 +16,7 @@
 ------------------------------------------------------------------------- */
 
 #include "msm_cg.h"
-#include <mpi.h>
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "gridcomm.h"
 #include "domain.h"
@@ -26,7 +24,9 @@
 #include "force.h"
 #include "neighbor.h"
 #include "memory.h"
-#include "fmt/format.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index ab2ec687d7..c99bbb2562 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -12,8 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "remap.h"
-#include <mpi.h>
-#include <cstdio>
+
 #include <cstdlib>
 
 #define PACK_DATA FFT_SCALAR
diff --git a/src/MANYBODY/pair_eam_he.cpp b/src/MANYBODY/pair_eam_he.cpp
index 0018429862..b0c4b7c205 100644
--- a/src/MANYBODY/pair_eam_he.cpp
+++ b/src/MANYBODY/pair_eam_he.cpp
@@ -19,13 +19,13 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "neighbor.h"
 #include "neigh_list.h"
 #include "update.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h
index 52b94192c2..a68dcc2198 100644
--- a/src/MANYBODY/pair_eim.h
+++ b/src/MANYBODY/pair_eim.h
@@ -23,6 +23,7 @@ PairStyle(eim,PairEIM)
 #include "pair.h"
 
 #include <map>
+#include <utility>
 
 namespace LAMMPS_NS {
 
diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp
index 14dacdae3f..05d9703443 100644
--- a/src/MANYBODY/pair_vashishta_table.cpp
+++ b/src/MANYBODY/pair_vashishta_table.cpp
@@ -16,11 +16,10 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_vashishta_table.h"
-#include <cstdio>
+
 #include "atom.h"
 #include "error.h"
 #include "force.h"
-#include "comm.h"
 #include "memory.h"
 #include "neigh_list.h"
 
diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp
index e369ab95e1..6226dd5ba5 100644
--- a/src/MC/fix_charge_regulation.cpp
+++ b/src/MC/fix_charge_regulation.cpp
@@ -32,15 +32,12 @@
 #include "improper.h"
 #include "kspace.h"
 #include "math_const.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"
-#include "molecule.h"
 #include "neighbor.h"
 #include "pair.h"
 #include "random_park.h"
-#include "region.h"
 #include "update.h"
 
 #include <cmath>
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index 4d481e7d68..ff49d84f6b 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -17,18 +17,19 @@
 
 #include "fix_tfmc.h"
 
-#include <cstring>
-#include <cmath>
-#include <cfloat>
 #include "atom.h"
-#include "force.h"
-#include "group.h"
-#include "random_mars.h"
 #include "comm.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "group.h"
 #include "memory.h"
 #include "modify.h"
-#include "error.h"
+#include "random_mars.h"
+
+#include <cfloat>
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index 520940f2f0..d78a6bcb95 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -33,7 +33,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index c94e91a0b5..559a56000e 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -30,7 +30,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp
index 85374e9214..ab081f8462 100644
--- a/src/MLIAP/pair_mliap.cpp
+++ b/src/MLIAP/pair_mliap.cpp
@@ -35,7 +35,6 @@
 
 #include <cmath>
 #include <cstring>
-#include "error.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index d56c875744..f8322fd9a1 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -17,19 +17,18 @@
 
 #include "dihedral_charmm.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index 09372f67ac..15e3aedc80 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -20,19 +20,18 @@
 
 #include "dihedral_charmmfsw.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
 #include "force.h"
-#include "pair.h"
-#include "update.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index ac31f906e0..38deee696e 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -31,7 +31,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index ad6202abd8..7d8cfdb90d 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -32,7 +32,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 242c33eb3a..0f1e813234 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -31,7 +31,6 @@
 #include "math_extra.h"
 #include "memory.h"
 #include "modify.h"
-#include "molecule.h"
 #include "rigid_const.h"
 #include "update.h"
 
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index ae0023ddec..64dc5ee9c6 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -25,7 +25,6 @@
 #include "tokenizer.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp
index 5c040da0f5..ae9d637180 100644
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@@ -22,21 +22,20 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_langevin_spin.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
 #include "force.h"
-#include "group.h"
 #include "math_const.h"
-#include "memory.h"
 #include "modify.h"
-// #include "random_park.h"
 #include "random_mars.h"
 #include "respa.h"
 #include "update.h"
 
+#include <cmath>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp
index 620d0a47bd..7bef18e9e7 100644
--- a/src/SPIN/fix_neb_spin.cpp
+++ b/src/SPIN/fix_neb_spin.cpp
@@ -27,7 +27,6 @@
 #include "comm.h"
 #include "compute.h"
 #include "error.h"
-#include "force.h"
 #include "group.h"
 #include "memory.h"
 #include "modify.h"
diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp
index c57feb8390..815ed2d290 100644
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@@ -22,20 +22,21 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_spin.h"
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
 #include "error.h"
-#include "fix.h"
+#include "fix_nve_spin.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
 #include "modify.h"
-#include "neighbor.h"
 #include "neigh_request.h"
+#include "neighbor.h"
 #include "pair.h"
 #include "update.h"
-#include "fix_nve_spin.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp
index d8d5632b06..647cb1e125 100644
--- a/src/USER-COLVARS/ndx_group.cpp
+++ b/src/USER-COLVARS/ndx_group.cpp
@@ -22,11 +22,8 @@
 #include "comm.h"
 #include "error.h"
 #include "group.h"
-#include "memory.h"
 #include "tokenizer.h"
 
-#include <cstdlib>
-
 using namespace LAMMPS_NS;
 #define BUFLEN 4096
 #define DELTA 16384
diff --git a/src/USER-DRUDE/fix_tgnh_drude.cpp b/src/USER-DRUDE/fix_tgnh_drude.cpp
index d8bf1d76f9..3cde93f1b5 100644
--- a/src/USER-DRUDE/fix_tgnh_drude.cpp
+++ b/src/USER-DRUDE/fix_tgnh_drude.cpp
@@ -24,7 +24,6 @@
 #include "error.h"
 #include "fix_deform.h"
 #include "force.h"
-#include "group.h"
 #include "irregular.h"
 #include "kspace.h"
 #include "memory.h"
diff --git a/src/USER-DRUDE/fix_tgnvt_drude.cpp b/src/USER-DRUDE/fix_tgnvt_drude.cpp
index 2339a6f9a7..ab566058d4 100644
--- a/src/USER-DRUDE/fix_tgnvt_drude.cpp
+++ b/src/USER-DRUDE/fix_tgnvt_drude.cpp
@@ -17,8 +17,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index ca13aac06b..50ebf8abbe 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -27,8 +27,6 @@
 #include "region.h"
 #include "update.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index bfdd85df49..436f6f56da 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -15,15 +15,14 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-#include <cstring>
-
 #include "fix_nve_eff.h"
+
 #include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "respa.h"
-#include "error.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "respa.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp
index f5358b5db1..1748530fba 100644
--- a/src/USER-EFF/fix_nvt_eff.cpp
+++ b/src/USER-EFF/fix_nvt_eff.cpp
@@ -17,8 +17,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 67ab3522ad..f8cb2a3d91 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -17,20 +17,21 @@
 
 #include "pair_meamc.h"
 
-#include <memory>
-
-#include "meam.h"
 #include "atom.h"
-#include "force.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
+#include "force.h"
+#include "meam.h"
+#include "memory.h"
 #include "neigh_list.h"
 #include "neigh_request.h"
-#include "memory.h"
-#include "error.h"
+#include "neighbor.h"
 #include "potential_file_reader.h"
 #include "tokenizer.h"
 
+#include <cstring>
+#include <memory>
+
 using namespace LAMMPS_NS;
 
 #define MAXLINE 1024
diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h
index de07d813b4..7672612c19 100644
--- a/src/USER-MEAMC/pair_meamc.h
+++ b/src/USER-MEAMC/pair_meamc.h
@@ -22,8 +22,8 @@ PairStyle(meam,PairMEAMC)
 #define LMP_PAIR_MEAMC_H
 
 #include "pair.h"
+
 #include <vector>
-#include <string>
 
 namespace LAMMPS_NS {
 
diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp
index ddeabd54db..4880b1303c 100644
--- a/src/USER-MESODPD/atom_vec_edpd.cpp
+++ b/src/USER-MESODPD/atom_vec_edpd.cpp
@@ -15,7 +15,6 @@
 
 #include "atom.h"
 #include "error.h"
-#include "modify.h"
 #include "update.h"
 
 #include <cstring>
diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp
index 04307429b4..147e5c322f 100644
--- a/src/USER-MESODPD/pair_edpd.cpp
+++ b/src/USER-MESODPD/pair_edpd.cpp
@@ -18,20 +18,20 @@
 
 #include "pair_edpd.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 <cstring>
-#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;
 
@@ -275,11 +275,9 @@ void PairEDPD::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)
+    error->all(FLERR,"Invalid random number seed");
+
   delete random;
   random = new RanMars(lmp,(seed + comm->me) % 900000000);
   randomT = new RanMars(lmp,(2*seed + comm->me) % 900000000);
diff --git a/src/USER-MISC/angle_gaussian.cpp b/src/USER-MISC/angle_gaussian.cpp
index 639d753afa..b8bd68bd02 100644
--- a/src/USER-MISC/angle_gaussian.cpp
+++ b/src/USER-MISC/angle_gaussian.cpp
@@ -13,16 +13,17 @@
 
 #include "angle_gaussian.h"
 
-#include <cmath>
 #include "atom.h"
-#include "neighbor.h"
-#include "domain.h"
 #include "comm.h"
+#include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/USER-MISC/compute_gyration_shape.cpp
index ac073d4cbc..12ccd84533 100644
--- a/src/USER-MISC/compute_gyration_shape.cpp
+++ b/src/USER-MISC/compute_gyration_shape.cpp
@@ -19,7 +19,6 @@
 
 #include "error.h"
 #include "math_eigen.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "modify.h"
 #include "update.h"
diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/USER-MISC/compute_gyration_shape_chunk.cpp
index e66173d704..2adfa4d2c9 100644
--- a/src/USER-MISC/compute_gyration_shape_chunk.cpp
+++ b/src/USER-MISC/compute_gyration_shape_chunk.cpp
@@ -19,7 +19,6 @@
 
 #include "error.h"
 #include "math_eigen.h"
-#include "math_extra.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"
diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp
index 98f699491f..c3144c084c 100644
--- a/src/USER-MISC/compute_pressure_grem.cpp
+++ b/src/USER-MISC/compute_pressure_grem.cpp
@@ -21,8 +21,6 @@
 #include "kspace.h"
 #include "error.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ----------------------------------------------------------------------
diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp
index 02e6d3e5da..eb90fd2dc4 100644
--- a/src/USER-MISC/dihedral_table_cut.cpp
+++ b/src/USER-MISC/dihedral_table_cut.cpp
@@ -29,7 +29,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 #include <fstream>  // IWYU pragma: keep
 #include <sstream>  // IWYU pragma: keep
 
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index 59f2560e0b..4bcc15933f 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -28,8 +28,6 @@
 #include "update.h"
 #include "variable.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/USER-MISC/fix_electron_stopping_fit.cpp
index b36984f3df..b3dbfb3337 100644
--- a/src/USER-MISC/fix_electron_stopping_fit.cpp
+++ b/src/USER-MISC/fix_electron_stopping_fit.cpp
@@ -20,18 +20,13 @@
 
 #include "atom.h"
 #include "citeme.h"
-#include "compute.h"
-#include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "math_special.h"
-#include "modify.h"
-#include "region.h"
 #include "respa.h"
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp
index ef6c390f95..6426eee5cc 100644
--- a/src/USER-MISC/fix_nvk.cpp
+++ b/src/USER-MISC/fix_nvk.cpp
@@ -17,14 +17,14 @@
 
 #include "fix_nvk.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "respa.h"
 #include "error.h"
+#include "force.h"
 #include "math_extra.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp
index 56da3cd6a1..ef68294fde 100644
--- a/src/USER-MISC/fix_orient_eco.cpp
+++ b/src/USER-MISC/fix_orient_eco.cpp
@@ -32,7 +32,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
index 18e1ed195f..54c6a0a9aa 100644
--- a/src/USER-MISC/fix_rhok.cpp
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -24,7 +24,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp
index 8a79b73034..84514526b1 100644
--- a/src/USER-MISC/fix_wall_region_ees.cpp
+++ b/src/USER-MISC/fix_wall_region_ees.cpp
@@ -27,7 +27,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-MISC/pair_wf_cut.cpp b/src/USER-MISC/pair_wf_cut.cpp
index d421049cec..451b3f1e49 100644
--- a/src/USER-MISC/pair_wf_cut.cpp
+++ b/src/USER-MISC/pair_wf_cut.cpp
@@ -25,8 +25,6 @@
 #include "memory.h"
 #include "neigh_list.h"
 
-#include <cmath>
-#include <cstdlib>
 #include <cstring>
 
 using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp
index c8db9cc98d..2ed5632fad 100644
--- a/src/USER-OMP/fix_nvt_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp
@@ -11,11 +11,11 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include <cstring>
 #include "fix_nvt_asphere_omp.h"
+
+#include "error.h"
 #include "group.h"
 #include "modify.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp
index 240825b2c6..6dc59b2db6 100644
--- a/src/USER-OMP/fix_nvt_omp.cpp
+++ b/src/USER-OMP/fix_nvt_omp.cpp
@@ -17,8 +17,6 @@
 #include "group.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp
index 6844729e92..17b932baf0 100644
--- a/src/USER-OMP/fix_qeq_comb_omp.cpp
+++ b/src/USER-OMP/fix_qeq_comb_omp.cpp
@@ -17,19 +17,19 @@
 
 #include "fix_qeq_comb_omp.h"
 
-#include <cmath>
-#include <cstring>
-#include "pair_comb.h"
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
 #include "memory.h"
-#include "error.h"
 #include "neigh_list.h"
+#include "pair_comb.h"
 #include "respa.h"
 #include "update.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 
diff --git a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
index 9a08cd284c..1637805081 100644
--- a/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_atomonly_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_full_bin_atomonly_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
index 816ebcb693..2e4ab6509a 100644
--- a/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp
@@ -11,14 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_bin_atomonly_newton_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
 #include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index 43b5e7e822..caea9e13d7 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_bin_newtoff_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index 600348ca73..188e936cc4 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_bin_newton_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
index 88a72c4594..d0c6841c3e 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_bin_newton_tri_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp
index 1e9b9369bd..a8d187d958 100644
--- a/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_multi_newtoff_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_multi_newtoff_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp
index 0bf79ff77d..61031c553b 100644
--- a/src/USER-OMP/npair_half_size_multi_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_multi_newton_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_multi_newton_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp
index 96b57cc7c6..8acfc0e3bc 100644
--- a/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_size_multi_newton_tri_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_multi_newton_tri_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
index 758eae2bd9..452a17fafe 100644
--- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -11,15 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_nsq_newtoff_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
+#include "error.h"
 #include "group.h"
 #include "my_page.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
index 6f9a3fbbaa..e63c564a0e 100644
--- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -11,15 +11,16 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_half_size_nsq_newton_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
+#include "error.h"
 #include "group.h"
 #include "my_page.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_halffull_newtoff_omp.cpp b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
index 088e490384..378859beff 100644
--- a/src/USER-OMP/npair_halffull_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_halffull_newtoff_omp.cpp
@@ -11,13 +11,14 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_halffull_newtoff_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
-#include "atom_vec.h"
-#include "my_page.h"
+
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/npair_halffull_newton_omp.cpp b/src/USER-OMP/npair_halffull_newton_omp.cpp
index 6ec75d2428..c9852b526f 100644
--- a/src/USER-OMP/npair_halffull_newton_omp.cpp
+++ b/src/USER-OMP/npair_halffull_newton_omp.cpp
@@ -11,14 +11,15 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "omp_compat.h"
 #include "npair_halffull_newton_omp.h"
-#include "npair_omp.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
+#include "npair_omp.h"
+
+#include "omp_compat.h"
 
 using namespace LAMMPS_NS;
 
diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
index 8f255ee1ba..9da74e36b1 100644
--- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
@@ -20,6 +20,8 @@
 #include "neigh_list.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
 using namespace MathExtra;
diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp
index 454a387982..28d64ca19f 100644
--- a/src/USER-OMP/pair_tersoff_mod_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp
@@ -16,12 +16,12 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
 #include "math_extra.h"
 #include "neigh_list.h"
-#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
 using namespace MathExtra;
diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp
index c12e3b9859..55bb7791a4 100644
--- a/src/USER-OMP/pair_tersoff_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_omp.cpp
@@ -16,13 +16,13 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "neigh_list.h"
-#include "neighbor.h"
 #include "suffix.h"
 
+#include <cmath>
+
 #include "omp_compat.h"
 using namespace LAMMPS_NS;
 using namespace MathExtra;
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
index 2e433a12ee..c0fef02a23 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
@@ -17,14 +17,15 @@
 ------------------------------------------------------------------------- */
 
 #include "pair_tersoff_zbl_omp.h"
-#include "update.h"
+
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
-#include "tokenizer.h"
-#include "potential_file_reader.h"
 #include "math_const.h"
 #include "math_special.h"
+#include "memory.h"
+#include "potential_file_reader.h"
+#include "tokenizer.h"
+#include "update.h"
 
 #include <cmath>
 #include <cstring>
diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp
index 23d7235578..daac740dbf 100644
--- a/src/USER-OMP/pair_vashishta_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_omp.cpp
@@ -16,10 +16,8 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
 #include "memory.h"
 #include "neigh_list.h"
-#include "neighbor.h"
 #include "suffix.h"
 
 #include "omp_compat.h"
diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp
index d6eda0f511..cfa98cea54 100644
--- a/src/USER-PACE/pair_pace.cpp
+++ b/src/USER-PACE/pair_pace.cpp
@@ -40,7 +40,6 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
 #include "neighbor.h"
 #include "update.h"
 
-#include <cmath>
 #include <cstring>
 
 #include "ace_evaluator.h"
diff --git a/src/USER-PTM/ptm_constants.cpp b/src/USER-PTM/ptm_constants.cpp
index 82bead2101..47d6d010f0 100644
--- a/src/USER-PTM/ptm_constants.cpp
+++ b/src/USER-PTM/ptm_constants.cpp
@@ -8,7 +8,6 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 */
 
 #include "ptm_constants.h"
-#include <cmath>
 
 const int ptm_num_nbrs[9] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX, PTM_NUM_NBRS_GRAPHENE};
 
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index e9d32b5684..4c9c469bda 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -22,7 +22,6 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "memory.h"
 
 #include <cstring>
 #include <Eigen/Eigen>
diff --git a/src/atom.cpp b/src/atom.cpp
index ecb82993ce..70ed5a3836 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -34,6 +34,7 @@
 #include "library.h"
 
 #include <algorithm>
+#include <cmath>
 #include <cstring>
 
 #ifdef LMP_USER_INTEL
diff --git a/src/atom_vec.h b/src/atom_vec.h
index ea2253d0c3..a1bd8fd812 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -15,6 +15,7 @@
 #define LMP_ATOM_VEC_H
 
 #include "pointers.h"  // IWYU pragma: export
+#include <vector>
 
 namespace LAMMPS_NS {
 
diff --git a/tools/lammps-shell/lammps-shell.cpp b/tools/lammps-shell/lammps-shell.cpp
index 6c8873093f..699062059a 100644
--- a/tools/lammps-shell/lammps-shell.cpp
+++ b/tools/lammps-shell/lammps-shell.cpp
@@ -11,7 +11,6 @@
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include <ctime>
 #include <fstream>
 #include <iostream>
 #include <string>
@@ -352,7 +351,7 @@ static char *plugin_generator(const char *text, int state)
 {
     const char *subcmd[] = {"load", "unload", "list", "clear", NULL};
     const char *sub;
-    static std::size_t idx, len;
+    static std::size_t idx=0, len;
     if (!state) idx = 0;
     len = strlen(text);
 
@@ -368,7 +367,7 @@ static char *plugin_style_generator(const char *text, int state)
 {
     const char *styles[] = {"pair", "fix", "command", NULL};
     const char *s;
-    static std::size_t idx, len;
+    static std::size_t idx=0, len;
     if (!state) idx = 0;
     len = strlen(text);
     while ((s = styles[idx]) != NULL) {
@@ -384,10 +383,10 @@ static char *plugin_name_generator(const char *text, int state)
     auto words = utils::split_words(text);
     if (words.size() < 4) return nullptr;
 
-    static std::size_t idx, len;
+    static std::size_t idx, len, nmax;
     if (!state) idx = 0;
     len = words[3].size();
-    int nmax = lammps_plugin_count();
+    nmax = lammps_plugin_count();
 
     while (idx < nmax) {
         char style[buflen], name[buflen];